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I would order a new CPU
They all seem fine, I even tested the other heatsink on it (just the temp monitor) and same result I think the SMC is not working correctly or picking up the temp sensors. but I have no clue how it can be flashed with a replacement one

I would consider ordering a new A heat sink unit. It's also possible the board itself is out of whack.
 
Even though it's unlikely can fix the issue. Did you try the SMC reset yet?

By the way, the CPU A may be around 10C warmer than CPU B. Since you can still control the fans, I suggest that you may use some fan control software to control BOTH fans with reference to CPU B temperature only. Just set everything with a 10C buffer than should be fine. Not an ideal solution, but at least should give you some protection from cooking the CPU (if the thermal paste application is correct).

Of course, I only suggest this work around if you really need to use the machine right now. And I highly recommend you avoid any operation that will stress the CPU (e.g. 60% usage or above).


Thanks for your reply, I'm having to use the Mac and have been for a while now, I have the booster fans ob both CPU's running at 1700RPM and the intake & exhaust fans on a fan curve so when CPU B gets hotter all fans speed increases.
This is my current fix but I still would like to know what is going on with CPU A's temps. I can see the CPU core temp from PCEIC its always displays false readings 95c+ but every 30 seconds or so it pulls in a plausible reading of 40C or 50C
This is my gauge at the moment. I have reset the SMC a few times and even removed the battery on the Logic board, all to not grate improvement. A side note PCI and Power supply fans some times idle at 2000RPM and wont return to normal
speeds of 600 and 800 until the SMC is reset once agine. this is proving to be very confusing as I have never seen this behaviour on a mac before.

This all leads me to think the SMC is corrupted or damaged in some way but there is no immediate way of flashing this with a new SMC version
 
I would order a new CPU


I would consider ordering a new A heat sink unit. It's also possible the board itself is out of whack.
I did think that but I took apart the heat sink the other day and used a volt meter to see if there was any electronic difference between CPU A & B heat sinks and they all had the same readings leading me to think that is is okay.
I'm still under the impression that the SMC is shot.
I think the actual board is okay, more of a software issue with the board
 
I would order a new CPU

I would consider ordering a new A heat sink unit. It's also possible the board itself is out of whack.

I did think about that as well (the CPU tray is faulty).

If it's CPU related, then swap CPU A and B will know the answer.

Also, he already try another heatsink. So it seems not heatsink's fault either.
 
I did think about that as well (the CPU tray is faulty).

If it's CPU related, then swap CPU A and B will know the answer.

Also, he already try another heatsink. So it seems not heatsink's fault either.

I did test that out, pain in the ass to do but CPU A cooler was on top of CPU A but CPU B Cooler was connected to the connector for CPU A Still had the same issue.

I cant see how a CPU upgrade would render the tray broken, I still think that the EFI upgrade tool broke the SMC.
Since the issue happened I have installed the 2 Quad CPU's and downgraded the EFI and it was still broken.
If the CPU tray is faulty then I have no idea why it happened during the upgrade
 
I think I just found the issue,
After looking into some Mac SMC forums I found this

Non flashed Mac Pro 2009
SMC Version (system): 1.39f11
SMC Version (processor tray):1.39f5

My flashed Mac Pro 2009
SMC Version (system):1.39f5
SMC Version (processor tray):1.39f5

Some How the System has a the same SMC as the CPU tray, according to forums there is no new SMC for the system
This must mean that the reason for the issue is that the SMC version is wrong...can this be downgraded ?
 
I did think about that as well (the CPU tray is faulty).

If it's CPU related, then swap CPU A and B will know the answer.

Also, he already try another heatsink. So it seems not heatsink's fault either.

Just so we're on the same page. CPU A and CPU B have different heat sinks, they're not designed to be interchangeable.

@Maverick2880, do you have access to another Tower?

EDIT:
Just checked, my 2010 5,1 has SMC 1.39F11 while my flashed 09 reports 1.39F5. You might try flashing back to 5,1, since it should work with both processors.
 
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Just so we're on the same page. CPU A and CPU B have different heat sinks, they're not designed to be interchangeable.

@Maverick2880, do you have access to another Tower?

EDIT:
Just checked, my 2010 5,1 has SMC 1.39F11 while my flashed 09 reports 1.39F5. You might try flashing back to 5,1, since it should work with both processors.

Already tried that, unfortunately same issue, I'm massively annoyed this has happened and I use Final Cut and Prem pro a lot and I'm concerned this will make the CPUs overheat
 
Already tried that, unfortunately same issue, I'm massively annoyed this has happened and I use Final Cut and Prem pro a lot and I'm concerned this will make the CPUs overheat

Short of trying it in another tower I don't have any ideas :(. I hope someone else chimes in.
 
^^^^Yes, I agree loosening the heatsink bolts can be a bit tricky. Why Apple designed unseeable bolts in a deep recess is beyond me:oops: Maybe a better hex wrench and try again?

Lou
 
The one piece long handled ones with blue plasti-dip on the end have always worked for me.

Done 4 or 5 of them with same one. No issues with stripping.
 
I am actually creating a 10.8 bootable USB as I type this, even though I really don't like this new OS-X much. I think Snow Leopard is a much leaner, meaner, faster OS-X... But you are correct, W3690 forces me to upgrade (downgrade :p) to ML.

I know this is an old post but did anyone ever figure out how to install snow leopard after the 5,1 firmware? If i do this i want to make sure i can re-install snow leopard at some point. Even if i have an image i can setup to restore snow leopard. Because my single 4,1 came with an older 10.6 snow leopard and apparently i would have to get a retail 10.6.4 special build and modify the plist. Well at least that's what i read on another post. It sure would be nice to know how to downgrade after the firmware and chip change. Because I wasn't planning on putting the w3520 back in just to downgrade the firmware for snow leopard.
 
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