Cool about the Knoppix. Glad to hear that.
Have you tried booting into Window's safe mode with the PCI card installed? That may be helpful to "teach" Windows that the new card is physically there and then a successive reboot into normal mode may have no errors. I've already had an instance or two like this.
Not sure about your bios, but maybe there is shadow, cache, PCI VGA palette snoop (disable this) or other settings that Windows is not liking.
Another idea is to try to boot to Windows with the PCI card physically installed and no monitors connected, to see if Windows boot alright then. If so, you could then plug monitors in, even while Windows is running.
Do you know which power supply you are using and how many watts it is rated at?