I don't remember what patch I actually started having issues either. It seems like it was after this last one. It may have been the one prior, hell I can't remember. I have slept since then.
There are a few, and I mean few, that respawn any enemy what so ever.
I think the respawn issue started for me after 1.2.
I just found another dungeon that has not been cleared that has yet to respawn and its been several months since I been there its Fort Amol.
They really need to fix the enemy and alchemy respawns.