It's when the sub moves in a straight line when there are large waves and doesn't follow the waves (flying boat). It's also applied to boats that don't roll or pitch much on rougher waters but still stay in the water.
This is actually a game engine issue and can only be addressed to a limited extent by any mods. Adjustments to the boats can only go so far, otherwise you start creating additional problems.
It requires both a modification to the boats AND limiting of the wave size / frequency you encounter
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"There are only two types of ships- submarines...... and targets" Unknown
"you wouldn't catch me on a ship that deliberately sinks itself"- comment to me from a surface sailor. 
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