Scripted commanding easily leads to totally broken/unresponsive direct AI commanding. I assume this is a systematic problem with priorities (direct commanding > scripted commanding > FSM commanding; see wiki for setUnitPosWeak for example), and might even be the real reason for some other tickets (e.g. problems with high command, but I'm not sure about that...). Anyways, this bug is critical enough on its own.
tl;dr: Direct commanding should have the highest priority, alas it doesn't.