What difficulty were you playing on (I've noticed changing difficulty can change things occasionally)?
I played the mission again just now. It happened like before. When the pirate cruisers arrived shortly after the mission started they were able to use their capital beams (green).
Again, however, when allied capital ship reinforcements came in (Copernicus, Capella, Olympus, etc.) came in, they never fired beams (those kind of ships were supposed to have blue beams I believe). Even if I directly ordered a reinforcement capship to attack an enemy capship it would only move in and attack with anti-fighter lasers (but never blue beams).
I even targeted allied capships and was able to target their beam turrets (so they had them at least).
So enemy beams could fire, but those of the good guys couldn't.