I've played this game more than a dozen times, and this is the first time this has happened to me.

In the Tower, down from the four warders, I've cleared out the throne room, and gone up through the torture chamber and down to the room where the teleportation rune is located. Normally when you pick up the rune there, the floor rune lights up and you can transport to the other (ie south) side. But the rune on the floor does not light up, so I can't get around that way.

I am completely trapped. Though I can get into the lever room on the other side of the throne room, I can't open the second (upper) door in the lever room to progress that way (north). And the bottom (south) door to the throne room is now closed, so I can't exit back into the area where the stairs up are located. None of the levers seem to open either of these doors. Actually, though the scripts say that doors are opening and closing when I use the levers, I don;t think any of the doors actually are opening and closing. In this game that I'm playing right now, I've never seen anything change with the use of any of the levers.

Basically I'm trapped. Any ideas? Anyone else having similar problems?

I got trapped in a bedroom near the bottom of Durlag's Tower once. Couldn't get out no matter what. I moved onto BG2 after that

sorry, loading an autosave is all I got.

I don't know how to help you right now, however when i got stuck near Spellhold in BG2 (due to a disappeared NPC) some folks on bioware forum helped me through a save game editor and i was able to continue the game... bugs like these are often well known on official forums, maybe the answer is just "changing a flag" away ;)

Yeah, there must be some global variables that deal with whether those doors are open or are closed. I know ShadowKeeper (for BG-TuTu) allows editing global variables in saved game files, so GateKeeper probably does as well. However, knowing which variable(s) to change is the tricky part. I would probably revert to a previous save before I would start mucking about with global variables; I would rather waste a small amount of time replaying, than find out later I had totally hosed my game by assigning incorrect global variable values (thus wasting even more time).