These types of issues are difficult to track down. It appears to be RFI/EMI related and may be something as trivial as the length of some traces in the PCB picking up harmonics from an external source in the computer.
That said, I use the 480W Antec TruPower supplies as well and have UPS/line conditioners on all my systems and do not experience these problems with ATI or NVidia cards.
But again, if it is a harmonic in the case, it is going to be difficult to find/reproduce for NVidia and/or ATI.
I'll do some switching of parts tonight and see what happens.