It's for this reason that I turned auto updates off. There was one round of updates that destroyed my computer: any application that isn't registered with Microsoft can't operate. It's so bad even IE (EFFING IE!!!!) can't start. For a while I was nervous since System Restore didn't seem to do anything. Two days later, System Restore managed to stick. I promptly made a restore point, backed up my files (especially my Witcher saves), ran CCleaner, then Defraggler, THEN turned off Auto Updates. No problems since.
I traced the problem to a bad update because after all those, I tried updating, again, and the problem reared its ugly head again. I didn't bother to look into what update exactly. That ordeal was enough for me to turn updates off permanently, and will probably do so in all PC's I will end up owning.