im going to do some testing tonight based off this thread i found in netkas' site, concerning the card running at PCIe 1.0 and 2.0 speeds. it says that the mac pro 3,1 wont even run at 2.0 speeds so this could be a clue.
however, by that rationale I should have seen different results when running the mac pro 6,1 smbios. however, that doesnt necessarily mean that it is actually running at 2.0 speeds.
im just stabbing in the dark at this point so this may be fruitless.
netkas thread:
http://forum.netkas.org/index.php?topic=8400.0
"Keep in mind that recent NVIDIA drivers enable PCIE 2.0 in OSX on 4,1/5,1 Mac Pros but not on 3,1. Booting into Windows it is easier to tell right away. Our EFI'd cards are the only ones running at PCIE 2.0, unflashed Nvidia cards are all stuck at 1.0. "