Thank you very much Manel
I have passed this onto ASUS and nVidia as it appears the issue is now isolated to ALL ASUS X38/X48 motherboards (regardless of BIOS revision), but only Intel X38/48 motherboards using BIOS 1197 or earlier.
With ATi cards the issue is slightly different. The card Reports that it supports Gen 2.0 x16, yet it only runs at Gen 2.0 x4
nVidia cards run @ Gen 1.1 x16 and report that they only support Gen 1.1 x16 support, but this is intentional as the driver prevents a BIOS bug causing issues.
John