Just so im clear, you start a mission and the sub just sits there.
Wont move forward, wont move backward - on the surfacing im assuming?
Have you tried diving and using E motors?
My thought is now, it might be a mod that is causing the problem but i really cant say for sure. You should see what happends when you accidently type in 1262 (snorkel) into the engine supercharge slot in the basic.cfg (super chargers are 1260 and 1261 - ive editd my basic.cfg far too many times to have the memorized
)
Mods aside, usually if a boat just sits there after giving the telepgraph an engine order, its a bug that is solveable by just a quick jolt to reverse, and then forward again.
But a boat just stitting there like a cork in the water is a new one on me.