Hello
I am having some trouble importing my Maya model and animation into Unity 4. I have managed to make it import correctly as shows below, with all the animations in the file playing well in the preview.

The moment I go into the Rig tab and assign it a Humanoid type and select Create For This Model, Unity seems to recognise all my joints ok but it deforms the mesh like below:
A few components of the model get shifted (eyes, ponytail) and when I preview the animations I can see that all the IK movements of the arms are offset from what they should be. This happens both with the forced T-pose shown above (which was not my bind pose) and when I reset the pose to its bind one.
Has anyone had a similar problem or has an idea of what may be causing it?
Thank you very much!
Ok so it seems that the mad deformations were linked to anything that had a constraint in Maya. Some port of the mesh were not bount but simply constrained to certain joints. Unity doesn’t seem to like it so I ensured that everything was bound and ALSO that all the joints were connected to each other and therefore children of the main COG joint. Having chains that are separate from the main skeleton is also something that Unity doesn’t seem to like.
In any case the Generic rig works very well as is, so I didn’t need to use the Humanoid mapping. You can create an Avatar Mask, attach your avatar skeleton by browsing it, the mask will have a list of all the joints present in the skeleton, you just need to tick or untick the joints you want to layer and that you will be able to use the layers in the Animator, without the Humanoid rig.
Gotta love Mecanim 
Happens to me a lot. The muscle groups get pulled around. Simply edit the Avatar and click the muscle groups tab where you should be able to sort this out.
Half the time my humanoids end up looking like racing cars and spaceships!!!