The PDF format contains complex transparencies and blending modes of various objects. Unfortunately Postscript does not support all the vast majority of these so in order to properly print to a Postscript driver you must select the Print As Image option in our Print Dialog box in AcroPlot Matrix.
We do expect to support doing this behind the scenes like Adobe Acrobat and Reader does in future versions but it likely will not be until after the major new release comes out in the fall of 2012.