Have you tried to duplicate the phenomena with "unlimited fuel" and "unlimited batteries"?
Just for clarification, when I mentioned "below surfaced" I was referring to the constant depth change when plowing the waves in heavy sea. Gazing at the boat progression I can clearly hear the boat switch back and forth between diesel and electric.
Is this a recent problem? Have you tried to reinstall the game?
I assume you are using the "course plotting" tool, ending at your final destination.
If you are doing everything right, then I can only think of two possibilities:
a) a "bug" in your game;
b) it's the Kraken (I've seen strange shadows on the water once or twice in SH4, knowing there is no vessel of any kind there
)