Upon countless hours of me throwing my head at this, I found myself with a list of things needed to be done for your mesh to work with Mecanim out of Modo.
1st. Limit the amount of position, rotation, and scale zero channels. I found that having multiple amounts of these channels in your joints, was causing some awkward joint behavior. i.e. All the joints balling up at the center because the “root” joint had too many position and scale zero channels.
Solution: Merge down your channels and delete any channels that have “0” in their values.
Solution 2: Recreate your entire skeleton. Cleaning each joint can be very tedious and time consuming and recreating the entire skeleton may end up being the best way to go.
2nd. I was having an issue where most of my avatar would appear Red in the avatar window. Mecanim will not recognize joints that do not have weights associated with them.
Solution: Add joints at the end of chains so you can delete them after a bind. For example have a Neck–>Head–> (delete)Joint. Then bind your mesh, as a result of this your head joint will receive weighting, and all you need to do is delete the (delete) extra joint you created at the end of your chain. I’m sure there is a more proper way of doing this, this is just the way I found that works for me.
3rd. This one is iffy, naming your joints with the naming convention of, joint_L, does not get read as well as, Left_Joint. I call that last one iffy because I have yet to confirm this with multiple skeletons.
4th. Under the Muscles tab my “Finger Open Close” and “Finger In Out” were rotating awkwardly.
Solution: Rotate your geometry and joints so that your character’s hand is parallel to the ground (palms down), not perpendicular (palms toward you). I had my character with his hands perpendicular to the ground and was getting my strange results. I simply removed the skinning, rotated the geometry 90* degrees as well as my wrist joint, re-skinned my rig and as a result fixed my problem.
I hope this helps anyone else using Modo or any other 3d software use with Mecanim in Unity 4.
Please ask any me any questions, I’m still new at this stuff but I will help as much as I can.