Maybe they changed something in a recent bios update? I've always had to do the following to enable pci-e 3.0 on my rive and rivf:
http://forums.evga.com/How-to-enable-PCIE-30-in-Windows-7-m1607292.aspx
HKEY_LOCAL_MACHINE/SYSTEM/CurrentControlSet/Control/Video
Step 8: Identify the correct registry folders for each of graphics cards you have installed. There will be one associated folder for each card installed. To identify the correct folder for each card, you will need to review the names of each folder within the “HKEY_LOCAL_MACHINE/SYSTEM/ CurrentControlSet/ Control/Video” registry directory. The folder associated with a graphics card will have three or more subfolders (depending on how many PCI-E slots available on the motherboard). The values listed for each subfolder will be 0000, 0001, 0002, 0003, 0004, and Video. Review only the subfolders labeled as "0000". You will know you have selected the correct "0000" subfolder when you see a registry labeled “DriverDesc” with a value that matches the graphics card you have installed. Example, the value in my “DriverDesc” registry value reads “NVIDIA Geforce GTX 680”.
Step 9: Right click on the folder labeled “0000”. Select “New”, then select “DWORD (32-bit) Value“, then enter “RMPcieLinkSpeed” for the name of the registry.
Step 10: Right click the “RMPcieLinkSpeed” registry you just created, then select “Modify”, then enter “4” as the data value and verify that the “Hexadecimal” option is checked under “Base”, and then select “OK”.
Step 11: Repeat steps 9 and 10 for each graphics card associated folder (named “0000”)
Step 12: Once you have completed creating the RMPcieLinkSpeed registry for each card, close the Registry Editor window and restart your computer.
Step 13: Once your system is back into Windows 7 operating system environment, run GPU-Z and verify that the “Graphics Bus interface” value shows PCI-E 3.0 for each card.
Step 14: Re-enable SLI -or- Crossfire as needed.
