Quote from TheMasterCaver
I wonder if the game (from the crash) is still running in the background; I've had some crashes while modding in MCP that leaves the game running even after the window is closed, only visible in Task Manager, and I have to manually end the process. Also, you can try deleting the "session.lock" file in the save folder; this file is used to ensure only one program can access a save. Restarting your computer may also fix the problem.
That doesn't seem to be the problem, it happened about 5 days ago, and I restart my computer every night. I also deleted the session.lock file, but it didn't help. Any other ideas?
EDIT: I fixed it, just copied and pasted ALL the level.dat files from a fresh world.