In most cases, nails are colored procedurally through the Mat Room.  The EZShaper script does not take that into account, so it will ignore original setups and replace it with it's new set.  And the EZShader set only uses clear nail polish settings.  If you are using the XML to define which shaders to apply, then you can set ignore for the nails within the file for your particular character, and just use whatever other node structure relevant for your needs.