Thats odd - Miki & Koji get the transparency maps for their eyelashes and eyes okay - some kind of multi-channel mixer with multiply operators, seems like a strange way to do things. Have a search around here for Transposer issues and over at: www.eovia3D.net  - thats also a useful place.

Mind you, once you've set everything up to your liking click on the shader tab in the Assemble room, click and hold the shader for your character and drag it into the shader browser. Then you can simply drag and drop the shader whenever you bring that character into Carrara (make sure to drag it onto all bodyparts that have a separate shading domain)