Loaded again my game with the disobeying Treasure Galleon. One thing I noticed when I swapped ships (to see if I can get it going) was, that the ship would only then show my flag, as soon as I took control and put out it's sails. There was NO FLAG WHATSOEVER before and my pirate flag would pop out of thin air. But unfortunately that didn't do the trick, for the godforsaken Treasure Galleon still wouldn't budge as soon as I went back on my Schooner.
To me it seems as if the ships, that don't respond after being boarded and taken are still used as if they would have struck their colors. This status apparently maintains until a new screen at sea is loaded. Why it worked perfectly fine with the bark .... I have no idea ... even though, wait a minute .... I gotta try something.
*loads game now*
..... ..... .....
*returns*
Okay, it just struck me what may cause the ships to freeze and I was right. The captain in command of the Treasure Galleon was one that recently joined me after I beat him. He was the original captain of the Galleon. So I swapped him with the captain of the Bark, which was captained by one of my own, regularly hired officers. And now guess which ship moved and which didn't. Now it was the Bark not moving, while the Galleon did as she was told. So the problem/bug at hand is that captains, whom one has beaten and persuaded into service, will not respond to any commands given as long as one is in the same screen at sea, in which he had them beaten.
However, this wouldn't be the game that we love, if for every problem solved/recognized their wouldn't at least be two others to raise their heads. After I landed at the nearest beach, I came a bit too close to some bush bandits, I had no intention fighting against. So I boarded my ship again ..... and the battle music (from hand-to-hand combat) was still played in the back. Even though that is a tune that you never hear in direct sail. The music in general doesn't work correctly. For example the problem with "fighting music" still going on, even though you have all enemy ships beaten or even taken, is back again.
Another very weird thing was that - as soon as I left the aforementioned shore - the Treasure Galleon would fly a pirate flag ... but it wasn't mine. The ship was still part of my fleet ... but it had a different pirate flag.
Remember the wrong thumbnails I spoke about? These wrong thumbnails always are the "anonymous" ones, normally used for ships that are not sighted yet. The Treasure Galleon, as long as it would not respond, had this thumbnail as well.
Bottom Line
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Look into Flags and DEFINETELY look into captains, who are persuaded to become your officers at sea. There is definitely something messy in that direction. Also take a look at the thumbnails, even though that might be because of the "captured captains" - when I had the Captains of Bark and Galleon switched, the Bark was displayed with an anon thumbnail, too. So it might really be caused by the not-so-volunteer-officers. Hell, maybe these captains are even responsible for the messy flags. Would make sense since the dubious captain was in command of the Treasure Galleon, when it showed a wrong flag. Also he was in command, when it didn't show any flag whatsoever and would only do so as soon as I swapped myself on it.