I wonder if this has anything to do with the way things work while testing (Aka not published). I ran into quite a few odd things with BOFF's and enemy NPC's while testing in the Foundry that seemed to correct themselves once the mission was published. The only thing I've been able to judge is the Foundry characters are really only good for one thing, making sure the triggers work. Outside of that it's better to publish it and try it on a normal character since so much isn't working right in the testing environment.
In game @kahn. Click my sig to see our fleet's website.