Hi,
Looks like transposition table causes serious problem in edgame (at least in my case). Recently my engine has seven pawns advantage over TSCP and the game ended up in a draw because of threefold repetition. I used to check if the best successor from TT will cause draw by repetition in current situation but that's not the case. Because of the fact that in endgame TT successor is often returned at root node and no further analysis is performed, my engine doesn't spot that returned move will alow opponent reply that will actually cause draw by threefold repetition. So I decided not to use TT when game state that will be looked up has already occured in the game or current variation (I've noticed that if state that has already occured in the game is looked up in TT it is common that game ends up in a draw). I don't know if it's good solution. Maybe You have some experience in using TT in the endgame.