I just came across this exact same bug, so I came here to report it. I believe the reason this bug exists is because if you jump off the ship you are teleported back on. The game seems to be checking your elevation, and if you hit sea level then you are ported back. There has not been an exception made for when you are at sea level but still on the boat. Please fix ANet, this one isn’t difficult.
Map: Cursed Shore
Quest: Ships of the Line
Character Level: 80
Race: Asura
Professions: Elementalist
Party: Solo
Does it reoccur: Yes