I've done some searching, but I couldn't find an answer to my problem. My problem is that when I order a ship to jump in, even if it's got the Beam-free-all event flag, it won't fire it's beams. If I don't make it warp in, it fires fine. I tested this with a Ravana, after jumping in it was about 3k from a Deimos, and it never fired it's beams, only turrets.
I changed the Ravana to three Rakshasas, coming from behind, ending up at 2k. None of the three Rakshasas fired beams, only turrets. The Moloch that the Deimos was dueling fired beams.
I am utterly confused by this. Is there something I need to do to enable ships to fire beams after they jump in?