I don't have it installed at the moment, but I played around with the minelaying sub when I had it.
I think you have to set up the TDC for a stern shot (the game still thinks it's a torpedo in the tube).
So if you don't set up the TDC it won't let you 'fire the tube', because it thinks it is outside the gyro range of the rear tube.
Give it a go and let us know how you get on.