Don't know the answer but really are anxious to hear the answers.
I have maybe the same problem with my son's pc. Got it second hand, put a gt330 in it. Thought allreday it was broken, when i booted i got a long sets of ticking sounds and after a while it switched to the on board. Worked a while in windows, than restarted with the bad gpu in it so i could have a look at my bios. Got in Bios for a sec or 5 than the picture got completely teared and unreadable and after that no picture anymore even if i reboot.
Firstly, you wrote "video output on motherboard". I take it you mean there is no output whatsoever, but the monitor is connected to the VGA (not an onboard VGA output).
Secondly, AGP has several voltage keys, do AGP the connectors on the card match exactly? Since you mentioned they are both 8x, they should both operate at 0.8V, but maybe the first one was 4x/8x operating at 4x (speculating here).
If something on the motherboard got damaged, that would be the southbrigde controller, but I find it quite hard to happen. Have you double-checked the monitor and cables?