I am also having difficulty completing this level.
Initially, I had the same problem as those above, and I was unable to access the "fix" mentioned above, so I had to go back from my last save and replay nearly and hour to get to the same point.
That did fix the initial problem (where my friends wouldn't join the party).
Now, they've joined the party, and I've talked with Atris, I've freed the guy in the tube, and I've fought the handmaidens (whew). But, I still can't leave Talos Academy. Every time I try to enter the ship (with my two friends), it says I need my friends. Well, I have my friends. Why won't it let me on the Ebon Hawk?
I don't know if I'm supposed to free the droid or not -- but all attempts at doing so end in failure.
Can someone tell me why I can't board my ship?
Thanks.