I had the same problem as the OP, Bairdotr was not in her cage, but her weapons and captives were there. The DLC is checked in the additional content in game. So this morning I deleted (Or moved all of the game info for Larian in the My Documents folder,) the profile, and save games folders. I relaunched the game which recreated all the appropriate folders and created a new profile. Now all is well. Bairdotr is in her cage where she is supposed to be. Now I'm not sure if you need to delete (or move,) the entire Larian folder, or if just making a new profile will work. I thought this would help everyone out with any of the new DLC companion problems.
I also removed the speed mod.
-Good Luck.
Last edited by Mr. Underhill; 18/09/14 10:35 PM.