I don't know why this is happen but here's the simple fix, it's a bit weird but worth it!
Thanks to gastovski !
After your save file reaching 15mb++ some people will experience this issue.
1. Make sure your mod is configured
2. Never overwrite your save, always click new save
3. Everytime you load your game, press `or ~ (console) and then type player.kill
4. After you get killed, just load your game again and its fixed!
remember to always click a new save while saving!