At the end of the "Cannons of Mona" chapter, when you've captured La Couronne, you report back to the vice admiral, and he complains unless you're the one sailing that ship rather than one of your officers. He tells you to return when you have complete control of the ship, so I left, swapped ship, returned, and he still wouldn't proceed to the next bit.
After reloading a saved game, I swapped ship before going to see the vice admiral. That put me in charge of La Couronne and one of my officers in charge of my super-xebec El Diablo. This time he did what he was supposed to do, leading to the fights with the Dutch, after which he took La Couronne off me and put me in charge of El Diablo instead. That is, he gave me a second El Diablo, rather inferior to the original as I'd bought several upgrades for that one. Oh well, since I couldn't keep or sell La Couronne, I sold the fake El Diablo instead.
After reloading a saved game, I swapped ship before going to see the vice admiral. That put me in charge of La Couronne and one of my officers in charge of my super-xebec El Diablo. This time he did what he was supposed to do, leading to the fights with the Dutch, after which he took La Couronne off me and put me in charge of El Diablo instead. That is, he gave me a second El Diablo, rather inferior to the original as I'd bought several upgrades for that one. Oh well, since I couldn't keep or sell La Couronne, I sold the fake El Diablo instead.