There used to be a bug with boats flipping over if they were in line with a portal, as if the invincible player really was zipping across the space and knocking them over. Not sure if it still does this though. Do they always flip over when docked in the same location?

I believe that the floating in air bug has to do with the position being saved when the waves are high. Happened to me once.

Might be my imagination, but I believe the waves do get higher now than they used to. Sailing my karve when the winds are high seems much more risky than before. Point the bow of the ship into the oncoming wave, not sideways to it, to reduce the chance of being flipped.

But I've taken to docking my ship inside a chest, or portaling home with it as well.