I have 3 characters hit with this bug, 2 of them I "fixed" it by deleting the Peregrine and Yellowstone that were stuck showing as the active ship, but my 3rd one has my Aeon showing as active and I'm not going to be deleting that. I remember seeing some post about another way to fix it back before the forum change but I can't find it now.
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Yep. That bug has been around forever. I do not think they have a clue on how to fix it...and the reason they probably never figured out how to allow us to inspect other player's equipment like you can in almost every other MMO. ;-)
The only reliable way to "fix" this issue is commission another small craft and set that as your active one, then pray it doesn't also take priority over whatever ship you want to use. This will, however, almost always result in the new small craft taking priority over a different set of ships, meaning you'll have to switch back and forth between active small craft too.
This works for your character sheet (U hotkey) in space, but doesn't work for your info window. I had heard that an older ship takes precedence over a newer one for what shows as active in your info window, but I've never bothered to try it to see. Obviously, even if it did work, you likely wouldn't dismiss an Aeon timeship and go to the expense of getting a new one just to fix this display issue.
I can say with absolute certainty it's not based on how old a ship is. On one character I tried dismissing the shuttle then getting a new one and the shuttle took priority again, I also tried dismissing the ship and getting a new one and the shuttle still took priority.