A 4GB 680 only runs at PCIe 1.1 bus speeds under Windows(Bootcamp) even if you flash it.
A "flashed" 2GB 680 operates at PCIe 2.0 bus speeds under Windows(Bootcamp).
It's time we put this misunderstanding to rest.
When flashed with a rom written for it, a 680 (or any Nvidia 6xx card, for that matter) WILL run at PCIE 2.0 in both OS's.
I think part of the misunderstanding has to do with the way this functions now.
In both OSX and Windows, the card runs at PCIE 1.0 until needed, at which point it switches modes into 2.0. So the only way to be 100% certain is to use a test that places a load on the card.
In Windows via Bootcamp, GPU-Z will show a card as being capable of 2.0 but running at 1 UNTIL YOU LOAD THE RENDER TEST.
Have a look at the images, these are from our GTX680 4GB running in a Mac Pro in Windows via Bootcamp. Note that GPU-Z only shows that card running at 1.0 to begin with, then running the render test it kicks in to 2.0. The render test is gotten to by hitting the "?" just to the right of the PCIE field.
You can observe the same behavior in OSX using "lspci" (Google is your friend)
Note that "LnkCap" shows 5.0 in both, but in first iteration, it shows "LnkSta" at 2.5, I then ran CUDA-Z which kicked the speed up for the second time where you see LnkSta at 5.0
01:00.0 VGA compatible controller: nVidia Corporation Unknown device 1180 (rev a1) (prog-if 00 [VGA controller])
Subsystem: nVidia Corporation Unknown device 102e
Control: I/O- Mem+ BusMaster+ SpecCycle- MemWINV- VGASnoop- ParErr- Stepping- SERR- FastB2B- DisINTx+
Status: Cap+ 66MHz- UDF- FastB2B- ParErr- DEVSEL=fast >TAbort- <TAbort- <MAbort- >SERR- <PERR- INTx-
Latency: 0
Interrupt: pin A routed to IRQ 18
Region 0: Memory at 9e000000 (32-bit, non-prefetchable)
Region 1: Memory at <ignored> (64-bit, prefetchable)
Region 3: Memory at <ignored> (64-bit, prefetchable)
Region 5: I/O ports at 3000 [disabled]
Capabilities: [60] Power Management version 3
Flags: PMEClk- DSI- D1- D2- AuxCurrent=0mA PME(D0-,D1-,D2-,D3hot-,D3cold-)
Status: D0 PME-Enable- DSel=0 DScale=0 PME-
Capabilities: [68] Message Signalled Interrupts: Mask- 64bit+ Queue=0/0 Enable+
Address: 00000000fee00000 Data: 4092
Capabilities: [78] Express (v2) Endpoint, MSI 00
DevCap: MaxPayload 256 bytes, PhantFunc 0, Latency L0s unlimited, L1 <64us
ExtTag+ AttnBtn- AttnInd- PwrInd- RBE+ FLReset-
DevCtl: Report errors: Correctable- Non-Fatal- Fatal- Unsupported-
RlxdOrd+ ExtTag+ PhantFunc- AuxPwr- NoSnoop+
MaxPayload 128 bytes, MaxReadReq 512 bytes
DevSta: CorrErr- UncorrErr- FatalErr- UnsuppReq- AuxPwr- TransPend-
LnkCap: Port #4, Speed 5GT/s, Width x16, ASPM L0s L1, Latency L0 <512ns, L1 <4us
ClockPM+ Suprise- LLActRep- BwNot-
LnkCtl: ASPM Disabled; RCB 64 bytes Disabled- Retrain- CommClk-
ExtSynch- ClockPM+ AutWidDis- BWInt- AutBWInt-
LnkSta: Speed 2.5GT/s, Width x16, TrErr- Train- SlotClk+ DLActive- BWMgmt- ABWMgmt-
Capabilities: [b4] Vendor Specific Information <?>
Capabilities: [100] #10de
Capabilities: [118] #3f
01:00.0 VGA compatible controller: nVidia Corporation Unknown device 1180 (rev a1) (prog-if 00 [VGA controller])
Subsystem: nVidia Corporation Unknown device 102e
Control: I/O- Mem+ BusMaster+ SpecCycle- MemWINV- VGASnoop- ParErr- Stepping- SERR- FastB2B- DisINTx+
Status: Cap+ 66MHz- UDF- FastB2B- ParErr- DEVSEL=fast >TAbort- <TAbort- <MAbort- >SERR- <PERR- INTx-
Latency: 0
Interrupt: pin A routed to IRQ 18
Region 0: Memory at 9e000000 (32-bit, non-prefetchable)
Region 1: Memory at <ignored> (64-bit, prefetchable)
Region 3: Memory at <ignored> (64-bit, prefetchable)
Region 5: I/O ports at 3000 [disabled]
Capabilities: [60] Power Management version 3
Flags: PMEClk- DSI- D1- D2- AuxCurrent=0mA PME(D0-,D1-,D2-,D3hot-,D3cold-)
Status: D0 PME-Enable- DSel=0 DScale=0 PME-
Capabilities: [68] Message Signalled Interrupts: Mask- 64bit+ Queue=0/0 Enable+
Address: 00000000fee00000 Data: 4092
Capabilities: [78] Express (v2) Endpoint, MSI 00
DevCap: MaxPayload 256 bytes, PhantFunc 0, Latency L0s unlimited, L1 <64us
ExtTag+ AttnBtn- AttnInd- PwrInd- RBE+ FLReset-
DevCtl: Report errors: Correctable- Non-Fatal- Fatal- Unsupported-
RlxdOrd+ ExtTag+ PhantFunc- AuxPwr- NoSnoop+
MaxPayload 128 bytes, MaxReadReq 512 bytes
DevSta: CorrErr- UncorrErr- FatalErr- UnsuppReq- AuxPwr- TransPend-
LnkCap: Port #4, Speed 5GT/s, Width x16, ASPM L0s L1, Latency L0 <512ns, L1 <4us
ClockPM+ Suprise- LLActRep- BwNot-
LnkCtl: ASPM Disabled; RCB 64 bytes Disabled- Retrain- CommClk-
ExtSynch- ClockPM+ AutWidDis- BWInt- AutBWInt-
LnkSta: Speed 5GT/s, Width x16, TrErr- Train- SlotClk+ DLActive- BWMgmt- ABWMgmt-
Capabilities: [b4] Vendor Specific Information <?>
Capabilities: [100] #10de
Capabilities: [118] #3f
I can not actually speak for any other 680 4GB cards but ours run at 2.0 in both OS's. They do not always show this from System profiler, but do if you know where to check. Also, any of the CUDA-Z type benchmarks or OpenCl OceanWaves bandwidth will also verify the actual speed.