This has been a problem for a while, but sometimes the game will change the order of your desired doubloons. Example: I have an accuracy doubloon in the 3rd slot but then after a while, it will suddenly be in the 28th slot and every other doubloon will be scattered in a random number as well. I noticed this often happens whenever you earn completely new doubloons.

There was exactly the same problem with sorting powers, so maybe it's a related issue?