I have an 8X PCIe core in a Virtex6HXT (version 2.5, the latest in 13.4).
It's configured for Gen2 but it's coming up Gen1. lspci -vvv reports that
both the core and the board are Gen2 capable. I've looked at the PIPE
interface in Chipscope and the board is advertising Gen1 speeds only.
Xilinx support said that there is an issue with Sandy Bridge chipsets and
that something had to be done in the driver, however they didn't know the
specifics. Has anyone gotten V6 to run at 5GT on a Sandy Bridge? What did
you have to do to make it work?

lspci -vvv

01:00.0 RAM memory: Xilinx Corporation Device 6028
        Subsystem: Xilinx Corporation Device 0007
        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, Cache Line Size: 4 bytes
        Interrupt: pin A routed to IRQ 12
        Region 0: Memory at e0000000 (64-bit, non-prefetchable) [size=256M]
        Capabilities: [40] Power Management version 3
                Flags: PMEClk- DSI- D1- D2- AuxCurrent=0mA PME(D0+,D1+,D2+,D3hot+,D3cold-)
                Status: D0 NoSoftRst+ PME-Enable- DSel=0 DScale=0 PME-
        Capabilities: [48] MSI: Enable- Count=1/1 Maskable- 64bit+
                Address: 0000000000000000  Data: 0000
        Capabilities: [60] Express (v2) Endpoint, MSI 01
                DevCap: MaxPayload 256 bytes, PhantFunc 0, Latency L0s <64ns, L1 unlimited
                        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 #0, Speed 5GT/s, Width x8, ASPM L0s, Latency L0 unlimited, L1 unlimited
                        ClockPM- Surprise- LLActRep- BwNot-
                LnkCtl: ASPM Disabled; RCB 64 bytes Disabled- Retrain- CommClk+
                        ExtSynch- ClockPM- AutWidDis- BWInt- AutBWInt-
                LnkSta: Speed 2.5GT/s, Width x8, TrErr- Train- SlotClk+ DLActive- BWMgmt- ABWMgmt-
                DevCap2: Completion Timeout: Range B, TimeoutDis-
                DevCtl2: Completion Timeout: 50us to 50ms, TimeoutDis-
                LnkCtl2: Target Link Speed: 5GT/s, EnterCompliance- SpeedDis-, Selectable De-emphasis: -6dB
                         Transmit Margin: Normal Operating Range, EnterModifiedCompliance- ComplianceSOS-
                         Compliance De-emphasis: -6dB
                LnkSta2: Current De-emphasis Level: -3.5dB
        Capabilities: [100] Device Serial Number 00-00-00-00-00-00-00-00