It was happening a lot with me in one of my system. I had to recover boot partition several times as my system was unbootable many time. In your case you get it fine after restart but for me, mostly had to recover boot loader etc. Though my hd was fine, but I think there was some problem in partition table + mbr !
And one day it was gone mad, I was not even able to recover bootsector. So finally I had to reformat whole disk. And from then its running fine !
Moral : may be mbr and partition table is corrupted. A fresh format and repartition, reinstallation can help you out. (only if you are sure that your hd is not the problem ie. its in good condition.)
