No problem, glad to help.
Hmm I never had a problem with AA gun.
If you had the AAguntodeckgun+Radio enabled, then the AI on your sub will only will only fire against surface targets and can only be manually controlled when at GQ and main deck gun is manned.
Unofortunately, the shortsighted devs never bothered to give us multipurpose AA guns(what the hell really?) which is terrible because that is what US subs primarily used their AA guns for, to attack smaller ships not worth torpedoes etc. Aside from Pearl Harbor and maybe two other instances, in all the reports I have read, etc, AA guns were not used against aircraft often.
Whenever mod it, its a either they function as deck guns, or they are AA guns and they are linked to the main deck gun and activated as deck guns. They wont fire if not manned. Ive tried to work around this but no luck.
I remember explaining all of this in the V1.0 README and a README included with the AAtodeckgun mod.
In TMO Update by default the AA guns are AA guns, but the mod can be enabled to have them as deck guns. In early war when onyl have one deck gun I keep them as AA guns but when get into mid to late war and have multiple AA guns...they along with deck gun can put quite a bit of firepower on a surface target. WIll shred the small boats and quite useful in self defense situation.
If assigned lifeguard duties I may keep them active as AA guns, since may need to move into shallows on the surface to get a downed pilot, cant dive, Airplanes coming in, rare though.