I finally got the Balor down and get the fourth gem. But I could not use the door behind him. Simply could not activate it. I think this is because a fire bat was laying around in the combat area. I absolutely cannot target his tiny, unconscious body to perform a coup de grace. I theorize it is the bat that prevents me from activating the door, but I can't be sure. Finally I just teleported out of there. However, the skull does not have any powers of the fire gem. I don't think Zuggt is responding as if I have the full skull, either. Edit: Ok, it WAS the fire bat that stopped me going through the door. But that's not why I'm missing the fire powers. I swear I have that gem. Edit edit: I was able to reload an old save before I had picked up the gem. For whatever reason, that allowed me to target the bat. Killed the bat first, then picked up the gem. That worked.
I'm not aware of any previously reported issues with the gems/orb, but the balor et al has been fraught with problems from day one - game crashes when he explodes, gem can't be found, etc. Glad you got it sorted, at any rate.
The same problem happened to me as well actually after I killed Balor. I am unable to pick up the gem or exit the area. I then rest in the area for like 8 hours after that the problem was resolved.
I have had the same problem, but i solved it by inciting combat and then just end it and i could pick up the gem.