If you set rudder amidship (to 0) then your sub is at the mercy of numerical intergration steps adding up any small deviations that the waves have on your sub. (real sea currents are not modelled in the game, but roll and pitch are) These small changes add up quickly when you have hight timecompression. A little bit to port, a little bit more to starboard, and somewhat to port again, and so on and so on.This would look like what could be described as a "random walk". There is nothing you can do about this. It would be the same in a real ship. That's why there should always be someone on station at the helm, or atleast an auto-pilot.
If you give the pilot the command to go to a certain course, then he goes there, but doesn't keep it. He just thinks, "Oh well this is good enough and takes a break/falls asleep. Until woken up again.
If you set a waypoint then the pilot is continuously stearing towards it. Only when it has reached it does the waypoint disappear, and is the boat left to the mercy of the calculation steps. If this is far away then the pilot does as his job requires of him. So, if you want to set a certain course, you might want to set a waypoint far away (on land if neccessary) instead.
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