I have been noticing that my 780Ti's are not producing the same amount of PPD for folding.  As I was researching why, I noticed that when I did a GPUID, the PCI lanes it has for each card do not match what my mother board says they should.  I checked my BIOS and they are all set for Gen3.  I have an ASUS Rampage Black IV Black Edition board with an 4960X for my CPU.  The GPUID I got yesterday it stated that the first slot was PCI x4 3.0, the second was PCI x8 3.0 and the third one was PCI x16 3.0.  Not sure why the first one is x4 when it should be x16.  I can pull some data when I get home latyer today, but I cannot figure why this is happening.  Any ideas?

How do I determine which?

Just looked at the specs of your board on newegg and it appears two of your cards should be running at x16 and the other at x8. It may be your CPU. Test all the PCI-E slots individually to see if they all register at x16 when under load, this will rule out the slots being defective, all slots should read x16 3.0 when loaded.

Grey_Beard
I will do that. It's an immense pain when everything is in a water loop. Need to install another quick connect before my GPUs like I have after, as this is how I drain my loop. Need to drain it soon anyway, so I will try this in a couple of weeks. Thanks for the help.

No problem. Your board does have PCI-E dip switches, you can disable the slots to test each PCI-E slot individually without having to tear apart your water loop. 

Report back with your results when you can.

pci-e bandwidth does not really affect folding PPD. You can fold off a 1x slot with risers and see little to no performance loss. You should ask the gurus in the folding section to see if they can help to nail down the issue your having.