Yeah the mobo should not be affected, I tried getting video output from the internal graphics while building my system too and it didn't work then either, so my GPU should have nothing to do with it. I just added that for context. 
My problem seems to be that I have to access my bios settings to activate internal graphics, but that seems to be too stupid to be true. 
FYI, I bricked my card by flashing new firmware to it. Should be completely fixable, but again I can't do anything without video output. 
Could it be a problem with using HDMI, instead of DVI or VGA?
I'm going to borrow a GPU from a friend tonight and see if I can get it to work via BIOS settings.