> I am doing this in a 1U box, so there is a pci 1u > riser card. Could it be the riser is bad?
Maybe, you could remove the bracket from a PCI card and try it with the case lid off and no riser for a test (and other slots if you have any).. Have a look for leaky capacitors while you're there, if you haven't already seen your fair share, look at http://badcaps.net/ident/