Extemely strange startup/program problem

I have an Inspiron 1520 with 32 bit Vista Home Premium.

The short version:
My startup list seems to have been deleted except for a few programs. I do not remember everything that was on the list, but now my computer seems slower, probably because some important housekeeping programs are no longer running. Besides system Restore, is there a way to get windows to repair itself?
If not, can I reset windows to factory defaults without having all my files erased?

Could I also maybe partition the end of the c drive and copy over my files, do a factory restore, then copy back my files, then delete and reclaim that partition?
The Long Version:
My problem started when I bought and installed morrowind GOTY edition. (This was store bought, not torrented, bootlegged, etc.) It installed well and I played it for a bit. The next time I booted my computer, the icons loaded as usual, but after the first three tray icons load, all my icons go white and are reloaded slowly. I checked online for a solution and found that I had to increase my Max Icons Cache, but to no avail. I then noticed that avast wasn't running in the tray. I used spybots to check my startup list and found out about the deleted startup list. I ran full system scans with adaware, spybots, and avast but found nothing.

I added avast back, as well as my touchpad and NVIDIA drivers, but the computer seems to run slower i.e. generating preview icons takes 2x as long. I want to try to repair windows somehow before I resort to a complete factory restore.

 

Have you tried a system restore? Not the factory restore or reinstall.