Adding PCI video card to ML350 G4

[CA1201366]

I added a dual output video card to an ML350 G4. I have two monitors connected so that I can run dual displays. Whenever I reboot the server, I lose the configuration and have to reenter the settings after Windows boots. Sometimes one monitor works, other times the 2nd monitor works, and other times neither works. Shutting the server down completely sometimes fixes the problem. It happens on every ML350 G4 server I try it on.
I was thinking that the on-board video was conflicting with the PCI video, but read that adding a 2nd video card disables the on-board video. Is this true? Any suggestions would be appreciated.