Resurrecting thread because I have this problem too, for about a year now actually. Same diagnosis: random portions of dungeon interiors will just make my character invisible for a while. I do not think it is a permanent, static modification of the dungeon itself which causes this, because often I experience the issue when backtracking. A room that didn't turn me invisible before will do it later as I return through it in the opposite direction, and if you wait long enough the problem seems to stop. A specific room I can remember having this occur in multiple times on multiple playthroughs is the room immediately after you free the bandit stuck in the spider web in Bleak Falls Barrow. Anyway, my observation leaves me to assume the problem lies with something temporarily affecting the character only. I think perhaps it is a combination of any SMP hairstyles with Enhanced Blood Textures, as people have reported the exact bug for that mod. Also, I've been using No Camera Collision for years, so it wasn't a solution for me.