[Arkcon]

Most people seem to agree, the order in which the ships are clicked to enter into formation is the order of the ships.

That's not a complete answer 'tho. I have tried to manipulate the formation, for example, to get the ship with the point defense in the right spot, and have it not work. Seems to have something to do with when the ship was created, or something even more subtle that I can't track down.

Reselecting which ship is the leader tends to resort the ship formation