Three words - they aren't foolproof. I manually saved numerous times this morning. Exited the game at "manual" save #20, came back and half hour later and discovered all of them were missing. They weren't anywhere in Steam or in C: My Games/ Fallout NV. I killed Steam, restarted it and #20 reappeared alone...as #1. Of course it was joined by the first quick save and auto save made - never mind I have deleted them numerous times.
I am having the same issue with quick and auto saves. I do use manual saves, but it irks me that quicksaves looks correct when I use the option and then go to load without exiting the game, but as soon as I exit steam and re-enter, quick and auto saves are reverted to really old ones.