Submerine
You have not said if the model performs normally as soon as you are back on the surface, but if it doesn't I have the following suggestions.
I like Mtronic and have used them in many of my models but they can (as do several other manufacturers), in the event of a power wipe out, go into reset mode and this can result in you losing the fwd/rev function. The ESC has reset to minimum throttle stick down and only one direction as a result. I guess its pot luck whether this is fwd or rev but rev seems to be the most common.
If you replace the BEC with a battery to power the rx this may help. You do need to disconnect the red lead from the ESC to the rx and still need to switch on the esc after the rx.
If it has reset you need to reset the controls whilst the two lights are flashing by pressing the ESC button and moving the sticks to their full extreems.
You will need to have capacitors across the motor terminals and also between each motor terminal and the case.
Your rx connecting wires and aerial should be as far away as possible from the high current battery wires and the wires from the motor to the ESC.
Doug has already suggested re rerouting the aerial and as you have this suggests a weak signal.
Have you done a range check with the Tx aerial down? You should be able to have control from at least 20' without any interference?
Please let us know how you progress.
Dave