I've had this problem before, but I can't for the life of me remember how I fixed it. Anyway, the issue occurs during the Leviathan escape. The second part of the fight with Malak triggers the conversation with Bastila and Carth prior to being brought on board, and afterwards, I'm stuck in that room with Malak, unable to progress.
I took everything out of my override folder to see if that would work, but that just made the game freeze as it booted up. It'll take forever to list all of the mods I have for the game, but I'm sure that if a specific mod can cause this problem, I probably have it.
If I remember it correctly, I had the same problem before when I just opened the door that directly leads to Malak. Once I went around the room he goes to and open the doors normally and not with the security-ability, it performed as it should. If you opened the door that leads directly to him, try going the "normal" way.
It's impossible to open any of the locked doors, so the only way to get to him is to go around the sides and enter the locked room from the back. And when I do, I kick his ass, and it triggers the conversation between Bastila, Revan, and Carth that they had on the Ebon Hawk before being brought on board with the Leviathan.