Perhaps some software you installed since the last time, Anti virus are famous for this, is now running in the back ground and interfering with the game?
Try a strict clean boot
http://support.microsoft.com/kb/331796
I have also heard of weird situations where if the game is left idle for a number of months that a reinstall is needed to make it work smoothly again. Not sure of the valididty of this, but I have seen enough posts were people claimed it would help to to ignore this.
Now, you can back up your data files folder so that mods are easy to reinstall. Just put it on the new install. Assuming it is not a mod that is really causing this.
Also, unchecking your mods and loading a save that had those mods on it is not a good test, you need to do this with a character that has no mods on it if your testing an unmodded game. I would be best at some point to make a character on an game that has no mods, even buff them up with the console to survive. Then, use that save to test mod mixes and such and not your main characters.