I have been able to kill all the snow trolls except for those in the building with Kerish. Is there a reason for this? All the salamanders die but not the trolls.

Since it doesn't affect the game, please leave them for a while.

Well I had the same problem. I can kill them only using death-spell. And gain 4500 exp for each troll instead standart 1400. Ctrl-Y doesn't kill them

CTRL-Y does not kill trolls and other regenerating creatures. It is a feature of IWD/BG. Such creatures wear MIN1HP ring to ensure this. You should apply only those effects, which bypass their resistance to death. In case of snow trolls, it is fire. Slashing them won't do anything.

Trolls inside die as usual. Trolls in Aquarium and under, near exit, wont't die. They don't fall and you can't kill them

Well, as it turns to be this is the Bioware's problem. Look at here:

http://forums.spellholdstudios.net/index.php?showtopic=24019