My suggestion here is the same as Monica's, don't open PDFs in Illustrator that were created out of some other application. When the PDF was opened in Illustrator, your printer probably got an error message that said something like "Unknown Gradient type. Do you want to open anyway?" While many graphics applications speak the Postscript language, they're all speaking different dialects of Postscript. They all have different features and different ways of working with those features. In other words, an InDesign gradient is different than an Illustrator gradient, so when you open a PDF in Illustrator that was generated out of InDesign, Illustrator may not always recognize the gradients.
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