When I had this problem, tech support told me to go back the the server I was on when this happened and try boarding the ship. It never worked for me, but I think they had taken down the server I was on in the time between when I had the problem and when I contacted tech support.
I came back into the game the next day and found everything working just fine again.
Best thing to do would be to go to every server and try boarding the ship, see if what tech support told me works.
If not... well, I don't know.
