Are you sure your xorg.conf is read and applied correctly at start up? Maybe your MinX, MaxX, MinY and MaxY never get applied correctly … (You probably want to try your values without TransformationMatrix first.)
Maybe the values from post #5 are worth trying ( “MinX” “11”, “MaxX” “4082”, “MinY” “5”, “MaxY” “4093”).
I will have time to go through the data later today.
Meanwhile - if you not already did - you may take a look at PenMount-6000-Controller-Installation-Guide and driver download page.