Hi all,
What you're discussing here sounds very much like what happened to me a couple of times.
The JSGME can get fed up with doing its job and simply mess things up.

Even if you're running just one mod the JSGME install might have gone corrupt and won't work correctly.
Especially if your JSGME install has been working hard for some time with a lot of activating/deactivating of mods.
Without knowing more in detail what is happening I'd suggest you have a look at the
How to Fix Mod Soup Issues by Webster
Can't say if this is the answer to your issues but it could be worth a try.