This use to only happen if the game CTD, or if I removed a mod that it was using.
Now it just seems to happen from playing them.
It's also very annoying because I have to:
Open Mash-clean save file
Open Mlox, re-do my load order
Open the manual pluggin re-order'er (have to move a few certain mods to certain places to keep things running smoothly)
Does this just come with the territory of having 200 + mods?