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I came across this thread on Apple's Support Forum...

http://discussions.apple.com/thread.jspa?messageID=10465608

The 4th to last post has the explanation of what to do. I have done this and so far so good, however it's only been about 2 days since I've done it (which equals 2 shut downs). My Mac Pro doesn't restart after selecting shut down EVERY time, but it does often, so I can't be sure it's fixed yet.

It's quick and easy and worth a shot. I'll post again if it starts acting up again after doing this fix.
 
This is my log during that period:
04-10-10 23:18:52 com.apple.launchd.peruser.501[170] ([0x0-0x5e05e].com.apple.iCal[636]) Exited: Killed
04-10-10 23:18:52 1PasswordAgent[210] Shutting down 1PasswordAgent 3.4.4 #30767 built Sep 29 2010 10:57:33
04-10-10 23:18:52 loginwindow[64] DEAD_PROCESS: 64 console
04-10-10 23:18:53 kernel systemShutdown true
04-10-10 23:18:53 kernel systemShutdown true
04-10-10 23:18:53 com.apple.autofsd[77] automount: Mount for UUID=ED1DAC49-5CB4-3F69-B8E9-342BBC20C5ED has no path for the directory to mount
04-10-10 23:18:54 com.apple.autofsd[77] automount: Mount for UUID=ED1DAC49-5CB4-3F69-B8E9-342BBC20C5ED has no path for the directory to mount
04-10-10 23:18:54 shutdown[1129] halt by royhochstenbach:
04-10-10 23:18:54 shutdown[1129] SHUTDOWN_TIME: 1286227134 581855
04-10-10 23:18:54 mDNSResponder[20] mDNSResponder mDNSResponder-214.3.2 (Apr 12 2010 19:33:48) stopping
04-10-10 23:18:54 com.apple.SecurityServer[33] Session 0x1a1e833 dead
04-10-10 23:18:54 com.apple.SecurityServer[33] Killing auth hosts
04-10-10 23:18:54 DirectoryService[13] BUG in libdispatch: 10F2521 - 1960 - 0x10004004
04-10-10 23:18:54 com.apple.SecurityServer[33] Session 0x1a1e833 destroyed
04-10-10 23:18:55 kernel Kext loading now disabled.
04-10-10 23:18:55 kernel Kext unloading now disabled.
04-10-10 23:18:55 kernel Kext autounloading now disabled.
04-10-10 23:18:55 kernel Kernel requests now disabled.
04-10-10 23:19:30 kernel npvhash=4095
04-10-10 23:18:56 mDNSResponder[20] mDNS_StopNATOperation: NATTraversalInfo 105004C08 not found in list
04-10-10 23:19:30 kernel Darwin Kernel Version 10.4.2: Tue Jul 27 21:17:17 PDT 2010; root:xnu-1504.7.60~1/RELEASE_X86_64
04-10-10 23:19:30 kernel vm_page_bootstrap: 1468846 free pages and 104018 wired pages
04-10-10 23:19:30 kernel kext submap [0xffffff7f80600000 - 0xffffff8000000000], kernel text [0xffffff8000200000 - 0xffffff8000600000]
04-10-10 23:19:30 kernel standard timeslicing quantum is 10000 us
04-10-10 23:19:30 kernel mig_table_max_displ = 73
04-10-10 23:19:30 kernel AppleACPICPU: ProcessorId=0 LocalApicId=0 Enabled
04-10-10 23:19:30 kernel AppleACPICPU: ProcessorId=1 LocalApicId=2 Enabled
04-10-10 23:19:30 kernel AppleACPICPU: ProcessorId=2 LocalApicId=4 Enabled
04-10-10 23:19:30 kernel AppleACPICPU: ProcessorId=3 LocalApicId=6 Enabled
04-10-10 23:19:30 kernel AppleACPICPU: ProcessorId=4 LocalApicId=1 Enabled
04-10-10 23:19:30 kernel AppleACPICPU: ProcessorId=5 LocalApicId=3 Enabled
04-10-10 23:19:30 kernel AppleACPICPU: ProcessorId=6 LocalApicId=5 Enabled
04-10-10 23:19:30 kernel AppleACPICPU: ProcessorId=7 LocalApicId=7 Enabled
04-10-10 23:19:30 kernel AppleACPICPU: ProcessorId=8 LocalApicId=0 Disabled
04-10-10 23:19:30 kernel AppleACPICPU: ProcessorId=9 LocalApicId=0 Disabled
04-10-10 23:19:30 kernel AppleACPICPU: ProcessorId=10 LocalApicId=0 Disabled
04-10-10 23:19:30 kernel AppleACPICPU: ProcessorId=11 LocalApicId=0 Disabled
04-10-10 23:19:30 kernel AppleACPICPU: ProcessorId=12 LocalApicId=0 Disabled
04-10-10 23:19:30 kernel AppleACPICPU: ProcessorId=13 LocalApicId=0 Disabled
04-10-10 23:19:30 kernel AppleACPICPU: ProcessorId=14 LocalApicId=0 Disabled
04-10-10 23:19:30 kernel AppleACPICPU: ProcessorId=15 LocalApicId=0 Disabled
04-10-10 23:19:30 kernel AppleACPICPU: ProcessorId=16 LocalApicId=0 Disabled
04-10-10 23:19:30 kernel AppleACPICPU: ProcessorId=17 LocalApicId=0 Disabled
04-10-10 23:19:30 kernel AppleACPICPU: ProcessorId=18 LocalApicId=0 Disabled
04-10-10 23:19:30 kernel AppleACPICPU: ProcessorId=19 LocalApicId=0 Disabled
04-10-10 23:19:30 kernel AppleACPICPU: ProcessorId=20 LocalApicId=0 Disabled
04-10-10 23:19:30 kernel AppleACPICPU: ProcessorId=21 LocalApicId=0 Disabled
04-10-10 23:19:30 kernel AppleACPICPU: ProcessorId=22 LocalApicId=0 Disabled
04-10-10 23:19:30 kernel AppleACPICPU: ProcessorId=23 LocalApicId=0 Disabled
04-10-10 23:19:30 kernel calling mpo_policy_init for TMSafetyNet
04-10-10 23:19:30 kernel Security policy loaded: Safety net for Time Machine (TMSafetyNet)
04-10-10 23:19:30 kernel calling mpo_policy_init for Quarantine
04-10-10 23:19:30 kernel Security policy loaded: Quarantine policy (Quarantine)
04-10-10 23:19:30 kernel calling mpo_policy_init for Sandbox
04-10-10 23:19:30 kernel Security policy loaded: Seatbelt sandbox policy (Sandbox)
04-10-10 23:19:30 kernel Copyright (c) 1982, 1986, 1989, 1991, 1993
04-10-10 23:19:30 kernel The Regents of the University of California. All rights reserved.
04-10-10 23:19:30 kernel MAC Framework successfully initialized
04-10-10 23:19:30 kernel using 16384 buffer headers and 4096 cluster IO buffer headers
04-10-10 23:19:30 kernel IOAPIC: Version 0x20 Vectors 64:87
04-10-10 23:19:30 kernel ACPI: System State [S0 S3 S4 S5] (S3)
04-10-10 23:19:30 kernel AppleIntelCPUPowerManagement: Turbo Ratios 1112
04-10-10 23:19:30 kernel AppleIntelCPUPowerManagement: initialization complete
04-10-10 23:19:30 kernel mbinit: done (64 MB memory set for mbuf pool)
04-10-10 23:19:30 kernel rooting via boot-uuid from /chosen: F0C98F22-2DBA-3736-922C-8496FB1F0164
04-10-10 23:19:30 kernel Waiting on <dict ID="0"><key>IOProviderClass</key><string ID="1">IOResources</string><key>IOResourceMatch</key><string ID="2">boot-uuid-media</string></dict>
04-10-10 23:19:30 kernel com.apple.AppleFSCompressionTypeZlib kmod start
04-10-10 23:19:30 kernel com.apple.AppleFSCompressionTypeZlib load succeeded
04-10-10 23:19:30 kernel AppleIntelCPUPowerManagementClient: ready
04-10-10 23:19:30 kernel Intel82574L::start - Built Jul 27In 2tel82501740 L21:3::s1tart:39 -- r- Bunuiniltn g onJ deuvicl e2 a7 2t 010 b9d0f0
04-10-10 23:19:30 kernel 21:31:39 -- running on device at b10d0f0
04-10-10 23:19:30 kernel wl0: Broadcom BCM432b 802.11 Wireless Controller
04-10-10 23:19:30 kernel 5.10.91.27
04-10-10 23:19:30 kernel FireWire (OHCI) TI ID 823f built-in now active, GUID 78ca39fffe20f402; max speed s800.
04-10-10 23:19:30 kernel Got boot device = IOService:/AppleACPIPlatformExpert/PCI0@0/AppleACPIPCI/SATA@1F,2/AppleAHCI/PRT2@2/IOAHCIDevice@0/AppleAHCIDiskDriver/IOAHCIBlockStorageDevice/IOBlockStorageDriver/WDC WD1001FALS-41Y6A0 Media/IOGUIDPartitionScheme/Customer@2
04-10-10 23:19:30 kernel BSD root: disk0s2, major 14, minor 2
04-10-10 23:19:39 kernel vmnet: VNetUserIf_Create: created userIf at 0xffffff8011c9f400.
04-10-10 23:19:39 kernel vmnet: VMNetConnect: returning port 0xffffff8011c9f400
04-10-10 23:19:39 kernel vmnet: Setting peer info for hub: 8, port: 1, rcv: TRUE, flags: 64
04-10-10 23:19:39 kernel vmnet: VMNET_SO_BINDTOHUB: port: paddr 00:50:56:ee:ce:74
04-10-10 23:19:39 kernel vmnet: Hub 8
04-10-10 23:19:39 kernel vmnet: Port 0
04-10-10 23:19:39 kernel vmnet: Port 1
04-10-10 23:19:39 kernel vmnet: Setting peer info for hub: 8, port: 1, rcv: TRUE, flags: 64
04-10-10 23:19:39 kernel vmnet: Setting peer info for hub: 8, port: 1, rcv: TRUE, flags: 579
04-10-10 23:19:39 kernel vmnet: VNetUserIf_Create: created userIf at 0xffffff8011c9f200.
04-10-10 23:19:39 kernel vmnet: VMNetConnect: returning port 0xffffff8011c9f200
04-10-10 23:19:39 kernel vmnet: Setting peer info for hub: 8, port: 2, rcv: TRUE, flags: 64
04-10-10 23:19:39 kernel vmnet: VMNET_SO_BINDTOHUB: port: paddr 00:50:56:ec:57:17
04-10-10 23:19:39 kernel vmnet: Hub 8
04-10-10 23:19:39 kernel vmnet: Port 0
04-10-10 23:19:39 kernel vmnet: Port 1
04-10-10 23:19:39 kernel vmnet: Port 2
04-10-10 23:19:39 kernel vmnet: Invalidating peer info for hub: 8, port: 2
04-10-10 23:19:39 kernel vmnet: VNetUserIfFree: freeing userIf at 0xffffff8011c9f200.
04-10-10 23:19:39 kernel vmnet: netif-vmnet8: Adding protocol 2.
04-10-10 23:19:39 com.vmware.launchd.vmware[75] Verifying and re-installing files from /Library/Application Support/VMware Fusion/thnuclnt
04-10-10 23:19:39 configd[17] network configuration changed.
04-10-10 23:19:39 vmnet-bridge[104] Dynamic store changed
04-10-10 23:19:39 vmnet-bridge[104] Started bridge for 0, en0
04-10-10 23:19:40 kernel vmnet: VNetUserIf_Create: created userIf at 0xffffff8011c9f000.
04-10-10 23:19:40 kernel vmnet: VMNetConnect: returning port 0xffffff8011c9f000
04-10-10 23:19:40 kernel vmnet: Hub 0 does not exist, allocating memory.
04-10-10 23:19:40 kernel vmnet: Allocated hub 0xffffff806f91b000 for hubNum 0.
04-10-10 23:19:40 kernel vmnet: Setting peer info for hub: 0, port: 0, rcv: TRUE, flags: 64
04-10-10 23:19:40 kernel vmnet: VMNET_SO_BINDTOHUB: port: paddr 00:50:56:f2:6f:cc
04-10-10 23:19:40 kernel vmnet: Hub 0
04-10-10 23:19:40 kernel vmnet: Port 0
04-10-10 23:19:40 kernel vmnet: bridge-en0: media 20 dev 0xffffff8010a89008 family 2
04-10-10 23:19:40 kernel vmnet: bridge-en0: up
04-10-10 23:19:40 kernel vmnet: bridge-en0: attached
04-10-10 23:19:40 kernel vmnet: Invalidating peer info for hub: 0, port: 0
04-10-10 23:19:40 kernel vmnet: VNetUserIfFree: freeing userIf at 0xffffff8011c9f000.
04-10-10 23:19:43 kernel SAM Multimedia: READ or WRITE failed, SENSE_KEY = 0x05, ASC = 0x24, ASCQ = 0x00
04-10-10 23:19:43 kernel SAM Multimedia: READ or WRITE failed, SENSE_KEY = 0x05, ASC = 0x24, ASCQ = 0x00
04-10-10 23:19:43 kernel SAM Multimedia: READ or WRITE failed, SENSE_KEY = 0x05, ASC = 0x24, ASCQ = 0x00
04-10-10 23:19:43 kernel SAM Multimedia: READ or WRITE failed, SENSE_KEY = 0x05, ASC = 0x24, ASCQ = 0x00
04-10-10 23:19:43 kernel SAM Multimedia: READ or WRITE failed, SENSE_KEY = 0x05, ASC = 0x24, ASCQ = 0x00
04-10-10 23:19:43 com.apple.autofsd[72] automount: Mount for UUID=ED1DAC49-5CB4-3F69-B8E9-342BBC20C5ED has no path for the directory to mount
04-10-10 23:19:43 com.apple.SecurityServer[26] Session 0x2000345 created
04-10-10 23:19:43 com.apple.SecurityServer[26] Session 0x2000345 attributes 0x30
04-10-10 23:19:44 com.apple.autofsd[72] automount: Mount for UUID=ED1DAC49-5CB4-3F69-B8E9-342BBC20C5ED has no path for the directory to mount
04-10-10 23:19:44 loginwindow[59] Login Window Started Security Agent
04-10-10 23:19:44 WindowServer[86] kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged.
04-10-10 23:19:44 com.apple.WindowServer[86] Mon Oct 4 23:19:44 Mac-Pro-van-Roy.local WindowServer[86] <Error>: kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged.
04-10-10 23:19:44 SecurityAgent[159] Showing Login Window
04-10-10 23:19:49 loginwindow[59] Login Window - Returned from Security Agent
04-10-10 23:19:49 shutdown[163] halt by _mdnsresponder:
04-10-10 23:19:49 shutdown[163] SHUTDOWN_TIME: 1286227189 978015
04-10-10 23:19:49 mDNSResponder[20] mDNSResponder mDNSResponder-214.3.2 (Apr 12 2010 19:33:48) stopping
04-10-10 23:19:49 DirectoryService[13] BUG in libdispatch: 10F2521 - 1960 - 0x10004004
04-10-10 23:19:50 kernel systemShutdown true
04-10-10 23:19:50 kernel Kext loading now disabled.
04-10-10 23:19:50 kernel Kext unloading now disabled.
04-10-10 23:19:50 kernel Kext autounloading now disabled.
04-10-10 23:19:50 kernel Kernel requests now disabled.
04-10-10 23:19:50 SecurityAgent[159] CGSShutdownServerConnections: Detaching application from window server
04-10-10 23:19:50 WindowServer[86] hidd died. Reestablishing connection.
04-10-10 23:19:50 SecurityAgent[159] MIG: server died: CGSReleaseShmem : Cannot release shared memory
04-10-10 23:19:50 SecurityAgent[159] kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged.
04-10-10 23:19:50 SecurityAgent[159] CGSDisplayServerShutdown: Detaching display subsystem from window server
04-10-10 23:19:50 mDNSResponder[20] mDNS_Register_internal: Shutting down, can't register 16 Mac\032Pro\032van\032Roy._device-info._tcp.local. TXT model=MacPro5,1
04-10-10 23:19:50 mDNSResponder[20] mDNS_Deregister_internal: Record 10006CB10 not found in list 16 Mac\032Pro\032van\032Roy._device-info._tcp.local. TXT model=MacPro5,1
04-10-10 23:19:51 mDNSResponder[20] mDNS_StopNATOperation: NATTraversalInfo 10082C208 not found in list
 
Just following up from my post on October 5th.

Since I did what was outlined in the apple support forums, I have NOT had this issue any longer. When I choose to Shut Down, it Shut's down.

It's definitely worth trying if you guys are still having issues.
 
Gosh, I know this forum is 5 years old, but I wonder if anyone has resolved this problem themselves, or if they're an original respondent on this thread. The apple forum link doesn't work anymore unfortunately so I have no idea what was suggested.

I have a Mac Pro 2010 running mavericks. I have an PC Nvidia GPU, so the Mac boots without a bootscreen. It had functioned fine previously but after a fresh install, it restarts when I select shutdown.
 
Gosh, I know this forum is 5 years old, but I wonder if anyone has resolved this problem themselves, or if they're an original respondent on this thread. The apple forum link doesn't work anymore unfortunately so I have no idea what was suggested.

I have a Mac Pro 2010 running mavericks. I have an PC Nvidia GPU, so the Mac boots without a bootscreen. It had functioned fine previously but after a fresh install, it restarts when I select shutdown.

Unfortunately, I never got this resolved. I'm still using my now 6 years old Mac Pro and it will still occasionally restart instead of shutdown. It seems to happen very randomly and sporadically. It was suggested that perhaps a stick of RAM might be bad which can cause strange behavior like this. I never bothered to replace the RAM and because the machine is now over 6 years old and this only happens occasionally, I don't even worry about it anymore.
 
Just solved my problem, or at least identified it. I had a 2010 Mac Pro that I added a couple of things to - new Nvidia GPU and a USB 3 Card.

It's just my backup machine so I wasn't too worried about it. I know it's happened in the past but I couldn't remember what it was that fixed it.

Anyway... As has been suggested, it was the USB 3 card that was the culprit. I had 2 cables plugged into it. One had nothing attached, the other had an external drive that wasn't powered on. I tried disconnecting the drive, but that didn't work. This time I unplugged the cable that isn't attached to anything and it shutdown.

I know the issue disappeared at some point last time. I think I may have unplugged the USB 3 card and later plugged it back in and the issue didn't return. May need to find a new driver or something.

I disregarded the USB 3 problem as nothing was actually plugged into the card but cables, but there you go... Sort of solved. At least I know what to target now.
 
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