Ok, so I recently switched out my Intel 925 motherboard for an ASUS P5N-E SLI. On the Intel 925, my 8800GTS 640mb ran in PCIE x16. But, when I put it on the P5N-E, my control panel says it's running in PCIE x8.
The ASUS P5N-E SLI is known for its notorious dual-card function to disable and enable SLI, as shown in this picture:
Right now, it's "supposedly" set for single-card setup.
This is what CPU-Z is telling me:
I've mailed ASUS and all they told me to do was to update the BIOS...but I already have the latest, so I just reflashed the BIOS and...nothing. Still running at 8x.
Nvidia Control Panel is also recognizing it in x8, and in a non-SLI setup.
(Oh, and when I was setting up my computer, I noticed a little chip on the connector. Seems like one of them had its connector half gone, but it still works, and it seems like most PCIE x16 cards have the same chipped connector. Hmm...)
1. It isn't the video card. You already found that the card properly syncs up to x16 SLI. If you wanted to be really through, you could pop the card back in that old motherboard and make sure the card wasn't damaged somehow (maybe a connector was damaged in the swapping...).
2. It has nothing to do with peripherals, OS, drivers, or anything. PCIe link speed is an interaction between the video card and the motherboard, using the motherboards BIOS, at boot-up. That makes the problem MUCH simpler (ok : one small possibility : other PCIe based peripherals messing the bus up. But I suspect you have none of those)
The long of the short of it : once you do the test I recommended to make absolutely sure it is not the video card, you can be certain it is THE MOTHERBOARD. NOTHING to do with software, and nothing to do with any other hardware components.
Now, with the motherboard, you can take the following steps :
1. Search EVERY bios menu. I know ASUS mobos have some settings for manually controlling PCIe bus clock speeds and other things. Never know what you might dig up.
2. Try OLDER firmware. You can flash to various versions of the BIOS for this motherboard to see if it helps.
3. Once you have done step 1 and 2 you now will know for certain the problem is hardware : your motherboard is bad (which I honestly suspect from the start). Have to RMA it or exchange it.