I have had something like this happen before, it turned out to be a failing hard drive, but here was the catch, the failing hard drive was caused by a failing motherboard, which was caused by a failing power supply.
I would definitely say first check your hard drive, make sure that you do a thorough scan of it and use a S.M.A.R.T. reporting tool. If there are any issues found, then also use tools that monitor the voltage from your power supply, fans, etc. and make sure that everything is running properly.