Are you sure no one was running FAW at the transwarp gate to kill the ship mobs? FAW will target and get the transceivers killed everytime whether you mean to or not. I've missed out on the good loot of that part more than once over someones careless use of FAW on that part.
In your post you where suggesting that you had problems in the second half of the space battle about the transmitters being gone, but your conclusion to the possible problem is that after updating tribble with season 4 your "ground combat" has been jacked. Umm, thought you had problems in space?!?!
Now, I have encountered a space battle glitch where the transwarp gate stays open spawning in a hell of a lot of Borg. But that's been a long time since I've seen that.