It took me nearly fifty turns to figure this out. When you have more than four sponsor planets within the five hex radius of a shipyard and you build a colony ship, the sponsor planets that can contribute population to the ship only displays the top four colonies in the Colony Ship Embarkation UI. There is no scroll bar on the side, which is why it took me so long to realise what was happening, and when you do scroll with the mouse wheel it is very slow to move up and down the list. Considering the rather limited number of planets you can actually get within a five hex radius (barring map editing) I think this UI should show up to ten planets before giving a scroll bar. Similar to the Trade Ship Home Planet UI
Note- I happen to have six planets sponsoring this shipyard, because they're within the five hex radius, is that a bug or a feature? See linked photos.