Why are transparent parts of ID file turning to gray in PDF?

The transparent parts of my InDesign files are going to gray boxes (x-ray looking) around them.  I have done hundreds, if not thousands of PDF's from ID without an issue and all of a sudden this is happening. Though I have already figured out and used a jpeg work-around for now, I am still searching for the answer as to WHY this is happening all of a sudden, without any updates or changes on my end. WHY??? Can anyone else can shed a light on this?  Thanks.

I guess the question is, has a recent automatic update in Adobe software (this happens in Illustrator CS5.5, too) created a change in how PDF's are processed through their software?  Nothing I have done is different or has been reset...have used all of the software since it's creation, so I'm not a novice whatsoever.  It appears that any shape that is created using the transparency/gradient feature in the software turns to gray in the PDF's when using the save as PDF internal software feature in every configuration (then opens in Acrobat Pro...not Apple Preview, which has it's issues).  This has nothing to do with jpegs or anything else that is placed in the file (my reference to jpegs in my question is how I wound up saving the original file so everything would be flattened).  This work around is not a solution for me.b I am trying to find out if I am stuck with this because of Adobe software updates or something changed recently.  I am not the only person that has posted this issue on the web, but wanted to go straight to Adobe experts to see if anyone could shed any light on it.  Thanks for your time.

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