PMP, do you happen to have any newer version of P5E WS PRO BIOS than 0802?
I'm having strange problems with a GTX280 & P5E WS PRO, using 0802.

When using 0801, I get PCIe 1.1 & 8X speed.
With 0802, I get PCIe 2.0 & 8X speed, better but still not 16X speed.
And on top of this, with 0802 I get ~30-60 seconds delay before cold boot-up (the 1st beep).
I replaced the motherboard, still no go

A 9800GX2 worked OK though, full PCIe 2.0 16X speed - and no delay at boot up.

If you have access to a newer BIOS than 0802 for P5E WS PRO, pls let me try it... this is driving me nuts.