Hey new skipper, welcome to Subsim, the living Silent Hunter manual! Exactly what kind of conning tower problem are you talking about? Both Trigger Maru Overhauled and Real Fleet Boat play with timing on conning tower upgrades, but the very upgrade process isn't precise, just as it was not really precise in real life either.
Each time you end your cruise at home base, the game's virtual blind chimpanzee tosses a dart at a virtual target, at least where he virtually thinks the virtual target is, since he's virtually blind. If he sticks the target you get an upgrade: conning tower, radar, deck gun, Bofors AA gun, new sub, who knows?
Now that conning tower upgrade might first be available in June 1, 1942. But if the virtual blind chimp doesn't nail the target on June 2 when you return to port, you're otta luck. Each time you return to port he tosses the dart for upgrades again. It's possible, but not likely, that the chimp will be more like a chump, take a bad attitude toward you and NEVER hit the target to give you that upgrade all the way to the end of the war. Be nice to the chimp!
Then, you might be talking about something completely different, in which case
I am the blind virtual chimpanzee here. How bout a banana?