When all my ships are loaded into the flag, I can't select the flag with the hotkey. If the ships are unloaded, I can use the hotkey and everything gets selected correctly (including the flagship). But if I use the hotkey when the ships are loaded for transport, the flagship does not get selected (though the camera does center on it) and I can't give it commands.
This might be a bug or it might be an accidental setting where non-combat ships don't get selected...?
https://app.box.com/s/5wpseio1w657mkqtuplr779u3rhexxu1(Save is "2605" but I did start it on 2608)