My impression is that LM’s first try at having boats respond to 3D waves when using the Ultra water setting is not very successful. I suspect it will be in time, but for now there is a simple fix.
Until I get around to updating all my AI boats with this fix, you can do it yourself by adding the line always_use_avg_surface=1 in the [contact_points] section of the sim.cfg for each boat you want to fix.
It should look like this:
This issue will likely need to be revisited when v3.2 comes out.