EASY FIX
In TMO there is an Optional Mods folder, when in port (Fremantle), open the TMO file folder and take the "aft deck gun only" mod out of the TMO optional mods folder and add it with JSGME and all your gun problems should be solved....I only play aft deck guns and never had a Gun Bug.
If you have a copy of TMO or download a new one you can take the mod out of that instead of deactivating everything in JSGME. Just add the 'aft deck gun only' mod last in you mod list.
You can remove the 'aft deck gun only' mod after you upgrade to another class boat or keep it, that's up to you.
Also as Mr. Vontrapp has suggested, you should add the TMO Small Fix mod...or you may have a Tambor class boat for the duration of the war.
"Mr." Vontrapp..........I couldn't even keep a straight face just typing that
Edit; Ooops, I didn't realize DrBeast pretty gave you the fix already, though I think the Gun Bug and Tambor Bug are two separate issues. I believe the Gun Bug has always been there, in stock and previous TMO's.