You got it, it's submarines. Got to where I could duplicate the gripe or confirm it wasn't bugged, start from the office, fire some torpedoes, proceed to a resupply base and refit, save and exit to windows, restart the game and reload the save. If the bug is there, triggers every time.
What I was trying to do was make "starting at tender" more realistic, for one thing add an actual tender next to the starting point, then a "nest" of friendly subs next to the tender with the player starting in the nest.
Apparently that's a no-no, any sub, one or multiple, triggers the bug every time, the first time you refit, save, exit, and reload. Any surface ship works fine, any sub freezes the gauges.
So for now until we know more, a tender and a tanker with the player between works fine, but don't use any of the submarines as docked ships.
