I have had problems like that in the past, the way i fixed it was to make sure the drivers (windows) +firmware for the Hard Drives was current.. that fixed my problem, I dont know if yours is similer but it seems to be that way. But before that even happened i was having issuse with the "hal.dll" file in the windows directory (HAL=hardware allocation layer) it was a quick fix but as for you im not sure (Note: If there is hal.dll (Driver) issues or is corrupt it tells you during boot time, [My way out was to use Arcronis Ture Image](GREAT SOFTWARE BTW) and went back 3days and applied drivers and firmware. Damn Microsoft Updates caused my hal.dll issues in the first place but that problem was only specific to me because of the drives i was using, the sytem board and the raid array on the board. So to help i put in a SATA II Raid controller in my free PCI-E slot but still let me know how it goes..
PS: I dont know if you have but a de-frag never hurts anyone
