Chances are those weapons were firing. However, keep in mind those models were not designed to have a 4th weapon. When the game cannot find weapon hardpoint data in the mesh for a particular weapon, it defaults to making a single weapon point in the center of the mesh. So it would not have been very noticeable as there would only be one flak/missile point that was within the hull, so you couldn't see the weapon flash either.
Regardless if this is the cause of your problem or not, you'll most likely want to edit the mesh for the TEC Starbase and Kol sooner or later so you can place the weapon points where you want them. Oh, and the Starbases all have multiple meshes for when their upgrades are purchased, so you'll need to edit ALL of them (assuming the flak guns are not tied to an upgrade themselves). Have fun.