Using PvP bot after it gets out of a BG it will completely ignore all mobs and just run on the waypoints until it dies. I think a recent patch made it so BGbot / PvE would work, but AV is a lot better with PVP bot atm.
Unable to post a log ATM as not on the same PC as my bot.
BUT i also have this trouble.
PVP / Questing for me tho.
Bot needs a restart after every BG to kill something (Even when it gets agro it ignores)
**EDIT**
Just gave BGBot / Questing
Now after an AV the bot WILL kill as it should when back to questing. But for some reason the BG bot likes to go just outside the cave in AV and sit there all game. So don't matter which you will loose lvling aint gonna be as good as it should