Add offmeshesconnection for successfull path will resolve your issue, problem in booty bay is that pathfinder don't know than he can use tunel to enter/exit (I forget why, but I cannot change that), but pathfinder found another path (by the water) current offmeshesconnection don't works, with next features, you add offmeshes connection to the tunel and WRobot will use it to enter/exit of booty bay.
Ofcourse this will not resolve all bugs