Character rig controllers and hierarchy mismatch when importing from 3DsMax

Hi guys. We just started working in Unity 2.6.1 and in the first couple of steps we managed to get stuck :P. The character we're working with is rigged and set up for animation (controller shapes, HI solvers and all the fun stuff that should be in a character rig) but as always if there can be a problem there will be one. When we import the character in unity, no matter if .fbx or .max the bone hierarchy doesn't seem to work at all although the animations are working correctly. We tried all the hints for the Unity import like using the trajectory key collapse, using .max files instead of .fbx and some more information we found in the forums. So could anyone help us to move at least a foot with its assigned controller? Is there something we are leaving out?