Twice now, I have had the "ship loading" window appear for the launching of one transport.
The first time I had completed two transports of a custom design, saw only one ship completion icon drop-down, selected the planet from the planet list (single click) selected the transport and clicked "launch" from the planet data window on the main screen, filled the transport and clicked "launch" on the loading window. The ship loading window came up again, so I filled it and clicked its launch button again. With all I could find it appears these actions were applied to both planets.
The second time I had only one ship completion (all that I expected - I am watching the planet list constantly). Again the ship loading window came up twice.
Points to consider: This is a game that has been saved and reloaded once. I can not do another save without it crashing, and I have autosave turned off.