This is what someone recommended on the official SW:KotOR forum:
http://swforums.bioware.com/viewtopic.h ... 7&forum=26
(Carth's awareness was too low and Mission's stealth too high for the traditional fix to work. I'm sure many of you have the same problem as I did. Out of frustration and sheer desperation I spent hours trying everything I could think of....and something worked. I figured out a way to fix the glitch on my own.
1. Have Carth and the main character wear Sand people uniforms (if they have any left)
2. Speak to Carth before bording the Ebon Hawk (use all possible speach choices.)
3. Turn on both characters shields.
4. Immediately after the mini-game, begin mashing the A and White buttons. You will hear beeps during the sequence. If done correctly, before the music starts, you will hear Mission say, "No one can see this Mission" and you will hear her stealth activate. At this point the movie will play correctly, though Mission will remain cloaked until the next time she is switched to your party. (Note: This may be the only step necessary to surpass the glitch, but I only successfully did it once and I fallowed all of the above steps. Also, keep in mind that it will take several tries, but you'll know your on the right track if you hear the beeps in the background.)
I realize the above fix seems kind of rediculous, but it was the only way I was able to fix my problem. I am so confident in the fix that I sent an e-mail to the lucas arts support line asking them to give my suggestion to any who ask about the glitch. Otherwise, i would have been thirty hours down the drain. Keep in mind that this will probably only work if Mission was the character you used. Anyway, I hope that this helps everyone who was in my shoes. Good luck, and may the force be with your button mashing.
Sincerely, Harvester of Sarrow
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I don't know if it works as I've never had the problem myself, but good luck.