I will not attempt to answer all your questions, still need to ponder the exact response.  However, IBL does have a tendency to washout shadow areas strictly because it is just a general, overall ambient lighting.  I would delete that immediately given your situation; I find no beneficial use for it in PP2012 unless you use it at extremely low values. 

Any active ambient channels present in the scene can produce bizarre results because ambient channels are designed to make your object "glow".  A prolific cheat back in earlier versions of Poser but not necessary in the current IDL Poser iterations.  Those I would also eliminate.  The vendor is trying to convey a mood using MAT Room tricks which does not fit into your workflow. 

As for the gray chips, I think BB has explained that situation thoroughly. 

I have come across the same problem with colorless images used for color input.  In most cases, I leave those alone unless I can come up with a better alternative.  BB might have an reasonable explanation about how to handle those connections in a realistic fashion.