I'm always amazed at the total lack of common sense of some people, usually the pressman who has the perfect press and nothing ever is wrong with it.....
Are the spots really on the plate, or does it just appear that way? When in the run does this issue appear? What happens if they clean the plate, properly, and start back up, or just examine the plate where the spots are to see is what is there?
It sounds like a dirty press issue to me with excessive paper dust going throughout the press.
To understand the Poly Plates, they are a Negative Plate in the fact that the black part of the plate is what is being imaged and the silver image is what is left. For the plates to have a problem like that, there would have to be something blocking the laser so it did not image in that spot. This is not impossible, but it would be in the same location and on every plate.
What other presses do you have and what are the size of the plates? Could you take a plate that was showing this issue and clean it, cut it down and run on another press to see if the problem was still there?
These things are not that difficult to track down if all have an open mind and just think logically.
Also, make sure they are not using any Etch on the press. I really don't think that would cause this problem, but Etch will attack and deteriorate the plate.