I checked BIOS ...
Is it the latest version for your board? Perhaps the earlier boad had a different BIOS version or hardware (AA) revision which provided more power to the USB ports (or at least more reliable power). Self powered USB HDDs can consume alot of power from a USB port especially on spin up (compared to say a thumb drive which doesn't have this problem) so I'd imagine your drive currently isn't being fully powered when it needs it and thats whats causing the problem.
Is there any way these USB drives can have their power augmented or supplied through an additional power socket on the case and if so can you try powering them that way?