@nitram: I think I seen stuff like that in C.Rolands thread some time ago (you might read the posts there - it's based on 3ds max, but the theory behind is the same). From what Iremember it could be two things (that actually could be connected to each other):
a) you screwed up the skin instance,
b) it's in-deed shader related.
I haven't spotted any problems like b) by my own, although I don't pay attention to avoid issues caused by that. Still, I read that this might be a problem. But from what I remember it's not the problem that you use shadered and unshadered parts at once - until you don't combine them two one mesh (don't ask me whether this is possible, that's just theory). The problem is more, that some properties of the meshs seem to be different when it is shadered, respectively when it is not. Now, when you have a shadered mesh that uses properties like an unshadered (or vice versa), it could come to trouble like that. Again: that's what I read and how I remember it. Can't serve with details, but it might give you a point were to start. You might try to disable the shader via nifskope and see whether that helps. If you can't do it by your own, I might then shader the whole leaderhead for you if you only provide me all maps (nrml etc.).
Now, don't ask me how a) can happen, but it seems like a leaderhead can highly distort if the vertex weights are completely screwed up or if some bones aren't assigned that actually should be. I even had the problem, that after nifswaping nifskope didn't 'map' the bones properly. That means that although a certain bone was assigned to the mesh in the exported nif, it wasn't after I pasted it into the other nif although the bone was present there as well. You might correct this manually, but I think you need to do that immideatly after the swap without closing nifskope and then reopen it. Also, some leaderheads contain several exemplars of the same bone. Must be some kind of bone transplantation. That's true for user made / modded leaderheads only, I think. Now, it still matters to which of the two (or even more) exemplars of the bone the mesh is assigned. You could try to fix that by editing the nif in nifskope by editing the children of the skin instance of the distorted mesh.
In conclusion, I think you can determine which of these two possible reasons is the case for you easily. If a) is true, the leaderhead is distorted in both nifskope and civ4. If b) is the problem, it is only distorted inside civ4, but okay in nifskope. At least if I understood and remember correctly what they said when I read about this...