Oh, I weighted the bones,
The rest of the rig is nearly perfect except for the shoulder bit. All the bones I needed are weighted to 1 while the others are in the .dae file with weight 0 like the Clavicle and the bones that don't start with M.
Actually this would probably be a good time to ask if the bones labled something like R_Upper_Arm Should be weighted and would that be my problem.