In lack of other options I tried it, and... it worked!!!
Just start again in the academy, challenge the Echani Guards, win the matches.... and AFTER that, free your comrades.
After that comes the Ebon Hawk... but it is no playable Level, it's a cutscene.
It seems that the game is unable to jump into the cutscene when you freed your comrades before you challenged the Echani.
Either way, its a bug that needs to be fixed.