That is the sort of thing you should have brought up in the beginning. I can't help you sadly. I use 3D max for my models so my knowledge is not transferable.
Did you parent the skeleton to the actual mesh? I am using an older version of Blender so ....I am quite sure the nif scripts for Civ4 only work with Blender 2.49, from the looks of it you're using 2.7 Blender or above, I am not sure the nif exporter works that well or at all in that case. Either way , from personal experience I can say that a model doesn't follow the skeleton when no weight has been given to a bone, meaning you need to assign a group of vertex to a specific bone.
Other than this I can't really say what's wrong I'd need more infos from you
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