PCIE dosent work after Windows 7 install

Hello,
I have an MSI motherboard with onboard video and have been running windows XP with a PCI Express Nvidia Geforce FX9600GT. I recently installed Windows 7 and during the install and up untill the last restart the PCIE video card worked perfectly. Now only the onboard video works? i have tried to uninstall the onboard from the BIOS and through windows and still nothing once i had them both installed and under hardware manager it listed both cards but said that the PCIE could not work unless i disabled the other one. Tried that and still no video signal.
I am pulling my Hair out could ANYONE please help me.......