I use Battle Engine Melody and some others for my RPG Maker game.
So far I've been able to overcome all the problems, until I got to the Active Time Battle. It's been great with the orange haired (default) guy as the hero, but the secondary character I changed, and, well... this will show you what I mean...
EDIT: The same thing happens with the monsters. Don't call me a noob... I have only been using this a day. I've tried looking it up anywhere for three hours!