I had created a 1-up postcard for a proof in InDesign, and then placed it in a second InDesign document 3-up. When I exported it to PDF from the 3-up document using "Fiery Optimized" settings, the resulting PDF was missing all outer glow effects. Looking at the PDF, the outer glow on page one was on the "Sacramento Investor" logo on the lower left positions, and on page two, on that same logo, plus the text on top of all the property photos
I packaged the doc and links, which are attached. As part of that process, I created a new PDF proof using the same settings -- that time, the outer glow DID appear. Following that, I exported the PDF again, overwriting the original, and the outer glow DID appear for that as well... so unfortunately, I don't have an example of the bad PDF to share with you.