Well we had that same sort of problem where things were lost, and it happened to 5 different hard drives (3 failed completly) and realised what it was rather late.
Especially since it has happend twice with no circumstances, it could easily be your powersupply, causing power surges on the hard drive.
It was on mine, and as soon as i changed it, no errors, no missing files, no corruption. This is because as soon as the hard drive kept crashing, doing weird things, it was because of a surge which was damaging the boot sector and files on the drive.
So simply get a new power supply and then re-install windows. You can get them for about £20, and bout 400 watts of power too. I assure you taht could be your prob. Its safe to do that than to wait until it goes again isn't it.
I definetly don't think a virus could have done that
Try that, honestly