It was doing this to me too. Not sure if I still does it with the new version, because I just don't remember.
I'll clarify what he meant by this: He put it on mixed-something, and it went around killing stuff while it waited to join the battle. It went to the BG, fought people and stuff, and left. When it left, it just stood there while it waited to join the next BG. It joins it fine and plays the BG fine, but it won't level right.
I had a similar problem. I had it on mixed-EOTS, and it would not go back to leveling after 1 BG. I think the problem is it still had the BG profile loaded because I saw it said "Moving to hotspot distance: 4500" and I was very close to the hotspot when I joined.