I am trying to make a set of arms for a first person shooter in Unity. I have a single mesh and single armature that has both arms in them (Made in Blender 2.54). I planned on controlling the two arms with separate actions. I spent the time to make a few animations for each arm. I exported the mesh and armature together as an .fbx, with “All Actions” checked. When my friend imported the fbx into Unity, it looked like it was going to work great. The arms where there with their texture in their default position just fine. Then, he went to run animations. For some reason, he can’t get the arms to play the animations correctly. If you can imagine a first person shooter, with the right arm holding a gun in the bottom right corner, in ours, the right arm moves all the way across the screen, almost touching the left arm. Also, he can’t get the actions to play on top of each other. Is this enough information to see some sort of easy fix? Do I need to supply a .blend and/or Unity code? Is the problem on Blender’s end or Unity’s end?
Incidentally I’m wokring through the same issue, Personally my problem is that the vercitc’s are losing their constrain to the bone when you parent them, so I have to paint them (Or asign groups or something) check out this thread, I would LOVE to just give you a strait answer, but I’m still looking for that answer myself 
http://forum.unity3d.com/threads/40908-FAQ-Getting-skinned-animated-models-from-Blender-to-Unity3D
Thanks for the post. That thread you linked has a lot of information that I wish was helpful. It just makes my brain hurt. I think I will go post this question on the Unity forums.