PDF Displays as AI File?

Hi All,
Since upgrading to Creative Suite 5.5 all PDF's saved from Illustrator are being displayed as AI files in the workspace instead of PDF's.
This is a problem because multi page PDF's are being treated as single page AI, makes it impossible to check the contents of the PDF without downloading it first (see attached).
Any ideas when this will be fixed Adobe Team?
Cheers,
Stephen

Okay, in Illustrator, I selected the objects that are causing the problem, and went to Attributes/Overprint Fill. They were checked. So I unchecked them. Then I made new knockout versions in .ai and. eps, making sure Overprint Fill was not checked for the white objects.
However, in InDesign, there is no difference. I made a new InDesign file, placed the newly created .ai and .eps files, and still, the white logo does not display in Overprint Preview and does not print.
I had another coworker try this process. I double checked, I am running Illustrator 14.0.0 and InDesign 6.0.6. She is running Illustrator 14.0.0 and InDesign 6.0.5, so she has not installed the InDesign update yet, and even without unchecking the Overprint Fill, she is able to display/print/PDF this same logo fine.
I'm very confused now.

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