My copy of GalCiv is updated all the way up to Retribution, and with the 4.1 update.
I started a new game just to confirm what I've been suspecting, and my suspicions have panned out. Here's my tech tree as it currently stands, specifically the Warfare sections:
As you can see from both images above, my Missile and Kinetics tech has advanced to the point where weapons that don't use Antimatter or Thulium are available, while I've neglected my Beam tech entirely. It stands to reason that if I build ships with carrier modules, my carrier fighters should equip either Phoenix Missiles or Mass Drivers, right? Well, apparently not.
The fighters spawned from my Carrier Modules come with Beam weapons, for some unfathomable reason.
The same goes for Interceptor drones which spawn from my Drone Carrier modules.
Yet somehow, the Guardian Drones which spawn from my Guardian Drone modules are working properly, packing Kinetic weapons.
I know I've been bitching about carriers on this forum for a while now, but at this point I think there's a real bug that needs to be resolved here. A little help, please?