Atton escaped from his Force Cage at Telos Academy. During his discussion with Kreia, he's talking just fine, but his cage is empty. After I regain control of the Exile, I find Atton unconcsious near Handmaiden. This didnt seem to mess things up any, but it was odd.

Yup, had that one too, reloaded an earlier save and then Atton magically reappeared in the tube...

I've played through the game several times now, and only twice has atton actually appeared where he is supposed to in that scene

Ooops!

(Query Statement) Atton, Attton? Are you there!?

(Smug Statement) I forgot to tell you, I reversed the game's codding, so Atton will dissapear and find his own way home!

When you arrived on Telos, did you have trouble with the TSF guy and the Ithorian coming and going through the door when you were under house arrest?

 

They always got stuck for me, except the second time I played through. And that same game was the only time when Atton got put correctly in his cell after being captured by Atris. Every other time he was outside in the hall, same as happened to you.

 

I wondered if something in the game's timing gets fixed (correctly or incorrectly) early on, and this carries through until you start a new game.