I ran all over too and even went thru the Ithorian quarters solo. I finally said to myself that it has to be a bug or I missed some plot development somewhere.
From playing KOTOR I remember the game asking about adding party members when leaving the Ebon Hawk, but I can't think of an instance where party members simply disappeared and had to be "manually" added back--except when leaving the ship or choosing between 3 or more characters outside somewhere.
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Yeah, KOTOR II has a lot of little **** **** bugs that are just plain disruptive of a smooth gameing experience.