Hi
I think I know what caused this, because I encountered this problem a bit later. When you first enter the Academy and surrender your weapons as first answer you are going into a broken script and a woophole of sort.
"Clicking on Aron gives 2 options both labeled as [Cheat node]. #1 is to jump to the Atris CP confrontation and I can do this as often as I want. #2 is to continue with Kreias' speech, and it doesn't seem to do anything. Clicking on Kreia does nothing.
All the handmaidens are in the positions they are normally after the talk with Atris and normal dialog options are available. Sparing is ok with the handmaidens, but Ba0-Dur is unconscious in a cell, and since they are released normal by a conversation there is no switch to release him.
T3-M4 is in his containment cell and can be conversed with the normal option you would get if you click on him in a normal location (Upgrade, program spike, repair, etc.) but there is no way to release him.
Attempting to board their ship gives the message that you cannot pilot the ship without your companions."
So the solution I found after some googling is that you MUST choose option 1 and then surrender your weapons. Good that It had Autosave from outside before the battle with the three HK-50's.
Now my question is. Is there fix included in 1.7? Did I install it right? Like I said above, the steps I did. Do I need to install any other version before 1.7?
So if there is fix for that already then I must messed up with the install...
But so far I got over this point and everything else seems to be doing ok.
Just one problem - right after leaving the academy and flying on the ship before choosing your first planet, you find Atton and T3 playing Pazzak in the main center room, and you talk to them and when I choose to play some Pazzak with Atton right from that scene my Armor (jedi robe) went missing after that, nowhere to be found(in the inventory). So I put new armor instead. Not really a major issue.
Thanks in advance