Do you just want the rebooting problems to go away? I have no idea what your problem is, but If you just want to have a faster boot up, and are annoyed by the messages regarding your hard drive at the bootup, I would try shutting the computer with Hibernate. It might improve the bootup speeds, it might not, but its worth a try if you don't want to actually spend alot of time troubleshooting the problem.
If you would want to fix the problem, although I have no idea how to, you should try reformatting. Preferablly, someone with more knowledge will come and help you fix your problem. Until then, if you want a faster bootup and don't want that annoying message, try hibernating.
6600GT PCI-E for sale/Trade. Check the FS/FT forums on tech-forums for details.