I am always crouched but not stealthed.

[SurpriseFatty]

cleaning orphaned scripts, reloading, removing recent mods, nothing changes this. Sneak button doesnt work. cant play my thief character.

 

[Seijin8]

I find that happens to me a lot using Real Flying.

 

You need something that triggers a new animation.  I use the "Sit down" animation from iNeed (bound to a hotkey) to make the character sit, then everything responds as normal afterward.