Also, tool tips for healing powers seem to reflect the shuttle numbers then.
I found a way to reverse it: Selecting another default shuttle fixes it back to my normal ship. The original default shuttlewas a captain's yacht.
Edit: Indeed the Captain's yacht seems to be the only one triggering this (tested with a Caitian Fighter and a Runabout).
Edit2: It is not completely reversed, though. My Commander Engineer slots has somehow been cut down to an ensign universal... and and ens eng, both of which are displayed as slotted with the same officer. They do share the same cooldown, though. For at least partially fixing that, I had to re-equip my boff.