I've had this problem before, it turned out to be a bad sector near the start of my HDD (Generally System files used on start up).

I fixed it by using SpinRite http://grc.com it fixes problems with spinning drives by detecting read/write problems and will either then attempt to fix it or flag it as unusable (it will attempt to recover the data before it flags the sector)

If you don't want to pay then I'm sure that some bay where pirates live will be happy to provide you with a cheapish copy.