When I'm playing the single player game with some AI in the mix (I've played alot with the numbers and specifics but to no avail) and when I send my ships into a hostile system to wipe out the pirates and such there is no attacking at all. The Gauss rifle fires (when the ship has enough antimatter) but the Flagship doesn't fire its regular weapons at all and neither do the frigates I build. The pirates and other AI ships can't fire at me either. Everything else works fine.
I'm running version 0.76[b].18 and well the game is no fun if things are not able to shoot at eachother.