Just wanted to let you know, I'm running into the same/similar issue. It only started part-way into the run, but I've discovered that if Invisibility (or Chameleon) is cast, and the effect would end while my character is crouched, the character model remains 'invisible' while the spell effect disappears as normal. If the effect would end while standing, it performs as intended. This carries over to other saves, including ones where the character was definitely not invisible.
I still have no idea what is causing this, and it's driving me up a wall. I've been searching up and down the internet, nothing yet.
EDIT: A breakthrough!
Long story short, disabling Legendary Mastery fixed the problem for me (at least it seems so for now). I believe that the mod's "chameleon while sneaking" bonus is the culprit in my case.
With my limited understanding, my take is that this kind of bug is very likely if multiple sources are trying to cause invisibility at once.
