Is the new motherboard the same model as the old one? Did you format your hard drive before installing the new motherboard? You don't always have to do this, but it does make for a cleaner upgrade (especially if the new motherboard is a different model than the old one).
Does the motherboard have a Via chipset? Some motherboards with this chipset need the Via 4 in 1 drivers installed before installing the video drivers.
Also, if the new motherboard is a different model than the old one, the drivers for the onboard components of the old motherboard should be uninstalled (especially the video drivers, if the old motherboard has onboard video) prior to installing the new board. This helps create less conflicts, and makes for a smoother upgrade.