Read this post could solve most of the problems you have for incorrect behavior in game, if the answer is not here, please post it in discussion section.

When a mod/DLC add a new script, the script will be saved into the save file usually located in "C:\Users\<YourUserName>\Documents\My Games\Skyrim\Saves" folder, when the script are changed by the mod/DLC developer, there is a chance left broken scripts in your save file(eg. "Autosave.ess") and cause unusual behavior of the game. when this happened, you might want to remove the old broken scripts from previous version(will post a step by step tutorial).

Link for the tutorial:
https://drive.google.com/open?id=0B_lxPJuRBVFoOHYxd0V2NTUzSE0

Link for the tool:
http://skyrim.nexusmods.com/mods/31724

If there are any other questions, feel free to post it.
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