Well, I have multiple accounts. Warrior/rogue/mage. I also like to have backups in case I use a skillpoint in the wrong skill or regret something I did on the game, etc. I rarely use the autosave since I'm switching between accounts regularly.
It could be the large number of saves.
What could also be a factor is how much youve changed the game from its original loading, I mean, how many items youre carrying with you, if youve displaced a lot of stuff. All the things the game has to keep track of.
Game cells reset in about a month.
You can try going to a small indoor place and waiting there for a game month + a few days, to reset all other cells to their original settings, Im told that can help.
Mind that I am not sure if these things are actually the cause, or if it will help, but I figure its worth a try.
Good luck