I have a similar issue when defending Kraka Drak as Kraka Drak custom faction (by Cataph) against various factions including Ork rebels, Wintertooth & Chaos rebels. Only two towers (the 2 immediately left/westwards of the northern gate) will fire their bolts. The other towers on the north & east wall will not light up in yellow or fire when manned by a single unit standing inside their capture/control box.

I cant even load the map. Just a field battle. no custom assets. Maybe its better that way if Kraka Drak has issues.