I am noticing that the scaling does not appear to be working correctly which might account for the deformation. Are there any known scale constraint issues?

You're right the joints seem to be collapsing in on the root joint for some reason. A buddy of mine is working on it and has found that if he brings it into 3DS Max and exports it, it seems to work but does complain about gimbal lock. Not sure if that suggests anything in terms of what the problem and potential solution is. Would love to find a solution on the Maya side of things but so far no luck. Thanks for all your help- I appreciate it!

The FBXs look fine when imported into Maya- just deformed in Unity.

Hmmmm...found a more recent version but am experiencing the same issue. Tried skinning through the hypergraph as well as selecting the root SHJoint, selecting hierarchy (below), selecting the mesh and binding. I feel like I'm doing everything right but...Including pictures of the non animated and animated model in Unity.

Ahhh...ok, I must have grabbed the wrong version when I set up my new PC. I'll look for a newer version and if I can't find it I will upgrade. Thanks for your help!

Hey Dustin thanks for your reply. I noticed that the freeze/preserve joint rotation prompt is not appearing after saying "yes" to the single hierarchy skeleton and thought that might be the issue. Any idea as to why this might be happening? Thanks!