Being a programmer does not mean being savvy with safe/good web practices and how computers work (rather, Windows) - a few programmers I work with, despite being competent at programming, are good examples of this
It's like asking CS postgrads at universities to look after the IT infrastructures, it just doesn't work in general
Throwing random phrases like "reformat my computers folder view kernel" just shows that
If your PC's in that bad a state you're making it out it is, it could well be rootkitted hence why taskmgr shows nothing obvious. If files really are randomly disppearing by themselves, you shouldn't even be running the machine in it's current state if you want to avoid more data loss.
I suggest you boot into a safe trusted OS from a read-only medium, e.g. Knoppix or Ubuntu live disks burnt from a working machine, backup everything important to USB drives or another LAN PC, then full reformat the HD and reinstall the OS. It's usually much much quicker than trying to disinfect the machine these days with some of the nasties out there
Of course, it could just be something simple like a failing HD or disk controller and we're all being overly paranoid