Hi all,
There's a lot of confusion regarding this and @MrConway has given use some more info now around how this works (info below) and apologised for the poor wording in the shop (should be changed soon) -
If you have BOTH a Black ship - either bought in the ship or won via crates - and a Non-Black version of the same ship then you need to play a single game in the Black ship first to unlock the 2500 Doubloon Mission. At that point you can ONLY use the Non-Black version to complete the 10x 250 doubloon missions to get all 2500 doubloons.
If you have ONLY the Black version of a ship - either bought in the ship or won via crates - then you can unlock the doubloon mission but you CAN'T complete the steps.
I have the Tirpitz/Tirpitz B and Massachusetts/Massachusetts B so I played a game in each Black ship and now I have the Doubloon Mission for both ships which can only be completed in the Non-Black versions of each ship.
I hope that clears up any confusion people are having.