Corrupt Windows Folder on boot

Hey,

I recently upgraded my PC and installed my copy of 7 Home Premium, it's an upgrade kit so it works that I do a fresh install of Vista (from a disc) and then upgrade afterwards. This worked fine before on my old rig.

When running it operates perfectly but if I turn the PC off and leave it for a while (say a weekend) the OS won't boot. ie, Bios posts, it gets the the loading screening, gets upset and then goes into recovery mode. Last time this happened it fixed itself. Just now, it has come up warning me that the C:\Windows folder is corrupt and the startup repair is apparently doing its job.

I have no idea what's causing this. A restart during use is not a problem, and turning the PC off on a night and then starting the next day is fine. My suspicion is hardware, but I checked out the HDD and it didn't seem to have any bad sectors or fragmentation issues.

I've created a boot disc from the digital copy I own and may reinstall Windows and see if that fixes things.

The only thing I can think of that was similar last time I did this was encoding a large number of video files and then sticking them onto my iPhone. I used Xilisoft, did a load and then shut the PC down to travel - rebooting leads to failure. Of course this might be just coincidence and the time gap might be the problem?

Any suggestions before I do this? Reinstalling is such a hassle and all.

Thanks a lot