May not be what your experiencing, but i've gone swimming off my War Galleon and done this. Often you end up under the surface and not visible even if they are looking where you would be at.
Zeppers lvl 40 - All mastered but lvl 21 cannons
Groggy McJones lvl 26 - All weapons quest/tp quest finished - avoiding story quest
http://pirates.teamofx.us