Trainer mostly works now, but missiles appear to be broken. Guns no longer subtract ammo when firing, so that works great, but missile launchers, both vertical and multiple launch, don't work anymore. They just finish the firing sequence and instantly reset without launching any missiles.
Try the latest trainer.
Exact same issue, as soon as I disable the option the ship can fire missiles again
Do you have a save game you could provide us so we can use that to have a look?
Drop into the game folder, select skirmish, select Carrier Strike group as your fleet