You are leaving it up to Poser to make random decisions that may or may not give you the results you desire.  Don't misunderstand the set up on the New Material Set Panel.  'Selected nodes only' refers to the nodes you have selected in the material room prior to clicking the '+' icon on the Library and it only saves those selected nodes.  Everything else is ignored and not saved with the MT5 or MC6.  Now, not replacing nodes, retaining nodes, deleting nodes, etc. are things that need to be modified within each Material file, this is where the hacking done.  Unfortunately, there isn't a set of instructions readily available that teaches the principles such hacking and I'm not sure how secure you are in making code changes in those files.