Same thing just happened to me!
I woke up in jail, couldn't repair my ship. If I tried to Launch, I'd get an error that the ship was engaed in flagship battle. Then it'd dump me in Port Royal. (I had been working out of Tortuga, woke up in Tortuge jail).
Only thing that got me going again was waiting for the timer to run out. Ship then went to 0 damage and speed, I could repair it & launch it again.
Weird thing was, I kept getting the occasional info at the top of the screen saying a navy ship was enabled for boarding, I'd hear winching and other sea sounds. Then it'd go away. Did this off and onuntil the timer ran out.
I submitted a bug report, for sure.
