I believe that that option is meant to choose what kind of
PCI Express 1.0 to run, 1.0 or 1.0a, only in the case your are not using the slot in 2.0 mode; I might be wrong on that, but i think i'm not!

No seriously, I have a HD3870 and it shows
PCI Express 2.0 in CPU-Z, if i remember correctly.
Fowler, i think what happened is that your southbridge chip got up on the wrong foot and decided to mess with your HD.
Did you try a complete format (ie not a quick one)?
P.s.: I tried the new beta
bios and it works ok, i noticed 3 additions:
1) in the
Ram Timings>Clock Setting Fine Delay i found a new setting carrying the self explanatory name "DLL mode" (sarcasm) with options 0 or 1 available.
2) Now all the fans are monitored for RPM, checked with Everest. Well i cannot say i'm 100% sure since i'm not using one of the fan connectors. But the ones i'm using work.
3) There's a new setting in the Voltage Settings page, it's for the CPU and it's called something like "Voltage add max limit" or something like that.
Didn't try to tinker... it's active only over 1.3 like the special add, and i'm running below that.
Sorry for the lack of details in the report, but i flashed the
BIOS at around 5 am before going to sleep

.... and now i'm not at home.