It is difficult to say exactly what is failing on the PCI Express bus, but please be aware that there are other devices that can use the same bus internally. That being said, if you have run video tests without issue, I believe you can rule out the video card itself. It seems likely that the issue may be with the board itself, and you may want to begin the search for a replacement (the board was manufactured in 2006 after all).
I would like to caution you as well, just because the system is working fine for now doesn't mean it will continue to do so for much longer. I highly recommend backing up any important data, and keep an eye out for any problems. Our software can only tell you there is a hardware problem, and it is up to you to decide on your next course of action.
Please let me know if you have any other questions.
Thanks,
Kris