Ok I've done some more investigating and have found that this

Problem happenes on cold boot, but if I reset the PC then I have PCI-E x16 2.0 transfer rate working and everything else is hunkydory.
Now, does anyone else on here have a G92 GTS with a P5E3?
Do you have the Cold Boot X4 2.0 or X16 1.0 PCI-E rate problems?
Thanks
John