Hm...tricky that, normally when a mod is deactivated, JSGME should load the default data stored in JSGME's "!Backup" folder. Did you get any conflict message when you installed any of the mods you are mentioning?
I would start with unplugging all mods, and then activate them one by one and see what conflicts where.
I personally never had any function or graphic just disappearing after deactivating mods, so i am a bit confused here.
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