new install issue

Ok Im setting up a new barebone kit and get windows installed perfectly on it, the only prolem is that after I load the cd that came with the motherboard ( the drivers cd), windows will no longer load without the assistance of a boot cd.. but if I do not install the drivers from the boot cd windows will continue to operate just fine…. any thoughts on how to fix this issue would be great. it almost looks like the driver cd when loaded and the drivers are installed will erase the master boot record.