Bear in mind that Nomad or What was using Blender 2.49. I have only really every used Blender 2.49 to make animation edits due to the type of issues you are running into with Blender 2.7 FBX export. It seems that the 2.7 FBX export is rolling the bones by 90 degrees or something - probably this could be resolved by editing the script but it could be complicated to work that out.
One option would be to do all the animation work in Blender 2.7 then save your .blend file with Legacy Meshes Format checked, then open in Blender 2.49 and export to FBX from there.