Thanks. I'll have a look later today.
The other thing I can try is to make my own object and apply your media and FX to it to see if the same problem occurs. At the moment I'm having difficulty getting any textures to show correctly on the object (the original binary version).
More news later hopefully.
Edit:Done some more testing using my own objects and I can't see much wrong with the shader. I suspect part of the problem is that your alpha map is just too bright so that you only see the hair and not what is underneath. Try reducing the contrast in your alpha map and see if that helps - e.g. try making the alpha of the hair (not the black parts of the alpha map obviously) various shades of grey till you find the levels you need.
One thing I tried was to load multiple copies of the shader and apply different copies to each limb (I guess - but haven't checked - that your object consists of various limbs such as "hair", "face", "scarf", etc). This means you can use different techniques, with their own effect constants, on different limbs. For example, you probably don't need alpha-mapping on the head. That way you might be able to remove the alpha test from the hair.
Let me know how you get on.