I recently tried to claim an Archon Class on a low-level character and not only did it not appear in my ship roster, but my personal shields also dropped to -1 as soon as I claimed the ship (despite still having my shields equipped). I tried it a second time and still no ship or personal shields, which seems to happen every time I claim ships..
You have to change character and go back to that same character, which puts all the ships are into the list and fixes the personal shields. On a plus; I now have 2 Archon Class Intel Assault Cruisers in the roster.
EDIT: It appears to also happen with Bridge Officers.
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In one case (rom-kdf) it's ended up with 2 shuttles "ready" and no way to switch between them.
I don't *think* I've seen it on a Fed yet.