Problem : You repaired your ship with permanent repairs up to 100% and highlighting your tillerman shows your ship to be pristine. Your tillerman will report you the "scuttled" warning message every time you repair your ship. Attempting to sail will fail.
Solution : Conducting an Emergency repair and await the emergency repairs to wear out. You can sail at the scuttle speed if you wish. Shooting your cannon may expedite this process and cut the timer for emergency repairs. After the Emergency repairs have worn out your ship will recheck the repair status and sail at the speed of a fixed ship!
Possible Cause : Conducting permanent repairs while your ship was scuttled and under the effects of emergency repairs.
Possible Fix : If the ship is scuttled and under the effects of emergency repairs allow the permanent repairs to take affect. Most likely locations to check would be in a routine for the emergency repairs or permanent repairs.
If there is a better forum topic for this thread, by all means move it there.

Solution : Conducting an Emergency repair and await the emergency repairs to wear out. You can sail at the scuttle speed if you wish. Shooting your cannon may expedite this process and cut the timer for emergency repairs. After the Emergency repairs have worn out your ship will recheck the repair status and sail at the speed of a fixed ship!
Possible Cause : Conducting permanent repairs while your ship was scuttled and under the effects of emergency repairs.
Possible Fix : If the ship is scuttled and under the effects of emergency repairs allow the permanent repairs to take affect. Most likely locations to check would be in a routine for the emergency repairs or permanent repairs.
If there is a better forum topic for this thread, by all means move it there.