Art,
This is very common in large format especially if the customer is creating the pdf’s in AutoCAD.
Unfortunately I do not know the Plotworks software that well.
I know that KIP has a transparency setting you can turn on that corrects the issue.
Kip also has a free software on their website called KIP switch, this will flatten the print allowing it to print properly.
Doesn’t, PLP offer support on this issue?
Greg