Error message at boot

My girfriend has a sony vaio laptop that has run fine for two years now all the sudden she was getting missing windows\system32\config\system error message at boot. She made no changes to her computer before this happend. She ran checkdisk and defrag about a week prier to this and everything worked fine untill the message appeared. I told her to use the sony restore disk and run repair. She did now she get a fat32 error. I am thinking the Hard drive is the problem but everything I find on the net refering to the original error says lots of people have had this happen but can not pinpoint the problem. Some are saying it is possible the motherboard is the cause. Has anyone encounterd this problem or heard of a fix?