"transparent" bounding boxes appear when printing from InDesign and Acrobat

Hi. I have encountered a problem with both CS4 and CS5 InDesign and Acrobat 9.0. Mac OS 10.5.8. When I print (artwork flattened before I create PDF with standard "Press Quality" from InDesign or Adobe Illustrator default from Illustrator) lighter areas that are rectangular shaped will appear on the color print. We use a rip and this appears to happen randomly. I have spent considerable time troubleshooting this...I have used every work around I can think of—to no avail.
1. What is this?
2. Why is this happening?
3. Is there technical information out there to help me get rid of it?
Thanks so much!

Solid areas of lighter color. I am not sure if our rip can handle live transparency. It is a Fiery 8e Release 2. I tried a solution from a previous post that suggested de-selecting the Pantone match option when I print and that did work.
The PDF's are high res. It has even happened on some PDF's that were created through Distiller as high res. I have seen this at the print shop I work at and also at the college where I teach design.
Thanks so much for your quick response.

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