Hawke, that situation has happened to me at well. The only thing is, it was doing that well before the garbage update. It usually happens only when i log out a couple times to switch pirates.
If I have to sail somewhere, I usually open up the map to navigate me to the island I want to go to, and at the same time look at the compass to sail around the enemy ships so I don't draw fire. Especially seeing as you can seem to hurt them but they can hurt you!
The only workaround I've been able to find, is logging all the way out to the desktop, and then going back into the game. For the record, I use Open GL, I have been since the Port Royal island redo I think. That was because if you used DirectX9, the game would crash before you even got into the game.
But for some reason, that was never Disney's fault!