I don’t know what’s going on, I’m sure though that it is something to do with Maya.
When I import my .fbx into Unity the mesh is fine, I can see all of the joints, just not the animation.
I have been down to just a basic skeleton with keyframes baked and not baked. I have rigged an FBIX which works amazingly well. Set the frames and baked it to export. Still plays in Maya but nothing in Unity.
If you have ever heard of a site called Mixamo, I’ve downloaded a free animation from there and it plays in Unity.
Now, the download they give you is a .fbx which is great in Unity. If I import it to Maya and just as quickly export it from Maya as a .fbx it seems fine, but the new .fbx doesn’t have the animation. That’s why I’m pretty sure there is something I’m missing in Maya, I do have Maya 2011 and I have a slight feeling it might be the version of the .fbx exporter, but I may be 100% wrong. Anything would help, if you want the file I got from Mixamo just to see if you can get it I’ll give it to you.
Thanks 
Are you using Unity 2.6? If so then it doesn’t work so great with FBX 2011 (Unity 2.6 is based on FBX 2010). Try exporting with FBX format set to FBX2010 from Maya - that usually helps.
Ha, omg…
I was just messing around in Maya and thought of that…Changed it and BAM. It’s all there!!
I was coming on this forum to tell everyone I figured it out, I was pleased however to see that you came up with the correct solution anyway!
Thanks a lot. Guess I’ll have to wait for Unity 3 for 2011 I guess. I’m pretty excited. 
I’m sure I’ll be back with more questions.
hi everyone there!!!
As i can see you know a lot about this issues with unity and i just want to know if you can help me with this one please!!!
i have a model in maya with animation and all that cool stuff, and there seems to be perfect, but once i export that model to unity it appears like smashed or collapsed, the animation is still there (sometimes not) but the main problem is with the mesh, im using maya 2011 and the FBX 2011.3 and Unity 3.3.
Could you help me with this?? I’d realy apreciate helpful hand!!!