I'm guessing you are going back to using the on board GPU on your motherboard? I would try removing the driver for the added ATi card (either from add remove programs, or the device manager), and re downloading and installing the driver for your on board video card - you should be able to get Windows to do this for you from the device manager (right click "computer" > properties > device manager > display adapters > ). Try doing this before taking the Ati card out.
If you still have trouble, boot the computer in safe mode (displaying via the old GPU) and do a similar job while in safe mode.