I have experienced this before. You have to claim the draw.
After you have repeated the same position trice, click the draw button, and it will be a draw. Normally, the draw button will offer a draw, yes, but if you are in a repeating position, that has been repeated trice, you can claim it if you want to have the draw.
I don't know why it's not just a draw after three repetitions though.
it has happened serveral times in games now and really needs to be addressed. I have repeated the position x3 x8 x15 and more and the computer will not registar the draw. any one else have this issue.
http://www.chess.com/livechess/game.html?id=62825120