Personally I would 'trust' render GC more and try and find what's going wrong in it... Mat GC is pretty much a workaround for people that don't have access to pro, render GC is what you should be basing your work on.

About the desat look, what's the makeup setup like ? I assume you are painting maps in CS3 and layering them onto the base texture in Poser ? If so, have tried doing the layering in photoshop itself (as a test) and then using the new texture directly ?