had this problem before and it's is unbelievably frustrating as you know. only happened once i got GWX so my guess is they fiddled with waves slightly. as you found out rightly when your ship goes through a wave you dive in a way and diesels cut out on you. diving and surfacing helps alot to maintain speed. here are some solutions that i have tried and work
change course by 20 deg+ because your boat bobs up and down at a certain rate depending on wind not the waves! i figured it out by thinking this shouldn't happen and looked at the boat sideways(it goes back and forth in simple harmonic motion). once you are out of the pastern it should be simpler sailing
dive and surface a lot which is annoying but can works
sail to the nearest port/get close to land. this will change the weather and hopefully it gets better
hope some of these help
