Ship has sunk now, but to add more information, the reason on the top right was "Damaged planks". All of our planks for repaired to full, and we even replaced every gunport and plank with a new one. We set the NPC crew to repair and they repaired all they could. We were under the limit for both weight and crew, and we also tried going over temporarily to see if it would reset the "damaged planks", but nothing worked.