In my experience with TMO in every class but the Tambor/Gar you are defaulted to deck guns being fore it has never tried to give me an aft deck gun in TMO or a fore deck gun if I run the aft deck gun only option that is TMOs cure for the "deck gun bug" it can effect a swap in either direction.
The OP did say if he merely lost the stern 5 inch 51 and can only replace it with a 3 inch or 4 inch on the stern(which the this class should always have stern guns in TMO) or if he lost the gun and it got flipped to fore.
It may actually be a different glitch if you start the war in the Tambor it might have come with a 5 incher but historically the Tambor/Gars where built with a stern mount able to take a 5/51 but they did not actually start mounting them until 1943 if the CO wanted one they came new with a 3 inch 50.Maybe TMO does not make the 5/51 available for the class until a certain date and if you start with one but get an upgrade before that date you will lose the one you have.
My advice would be if you got lucky and started the war with a 5/51 on your Tambor class then turn down upgrades until 1943 to be sure that you don't lose it.Also you should avoid taking lots of damage this kills your renown and results in you getting crappy upgrades maybe they took the 5/51 because you are taking to much damage.
You might also want to try and test the default deck gun position options it might be a bug that occurs when you have a Tabmor class but also have the stern deck gun gun option also in use try using the default TMO mode and see what what happens then.