This also happens to me, but what I have discovered is this: It actually does clear the turn order, but all the names remain in the window. What I mean is that the text remains, but if you use the arrow to advance through the turn order, you'll find that it won't advance. If you roll initiative for another token, the turn order list will clear and you'll only have the new token(s) you added. It's been like this for a little while, I think. I've just gotten used to not using the -clear command and clearing the list the old-fashioned way.