Landing on islands sometimes spawns me underground, although unlike alpha, I'm not able to just swim out to sea and pop back out into the overland. I've been swimming in the water on port royal and the land just isn't solid so I can't run up onto it, i just swim right through. This is fixed by logging out and logging back in, however.
This is problematic for places like kingshead - I've landed there a handful of times and I've been underground every time, which basically completely removes my access to that island.