I'm having much the same issue, though a little more severe than what’s described above. Autosave and Quicksave get lost any time I exit the game. Strangely those slots work fine during a given session. The game saves to them and I can load from them just fine. But if I exit without saving to one of the main slots or, worse yet crash, then they revert back to where they were after my first hour of play. In my 10 hours of total play time, about 3 to 4 of them have been spent redoing stuff over and over again because of this bug and crashes.
In case it helps, I’m running Windows 7 64bit.
I had that same problem, even after they say they fixed it. However, I deleted both save files(auto and quick), disabled Steam Cloud(Not helpful if you're not using Steam), restarted Steam, opened the game to verify my saves weren't back mysteriously, and jumped in my save file.
I proceeded to fast travel a couple places to get an auto save in, hit a quick save, and saved manually.
After that, I exited game, opened it back up, and saw my saves were now brand new, up to date saves. I also repeated the previous step and force closed FNV through Task Manager to simulate a crash(I think?) and opened the game to check to see if my saves were still intact, and sure enough they were up to date, up to the point I ended the process.
May help you, may not. Those are the steps I took to actually get mine to get back to work and out of Primm.