Illustrator CS6 does not save PDFs to artboard

I have had this problem more than once. The first time it happened, I uninstalled AI and did a fresh install which fixed it for a short time. When I save a PDF out of AI, it does not save to the artboard constraints.
This is a screen shot of my AI document which has 2 pages.
When I save as PDF, this is what the file looks like:
(Pg 1)
(Pg 2)
After the original file has been saved (incorrectly) I can open it and save it again and it will be fine. Any ideas?

Here's my test of a similar file in AICS5
and here's the PDF
Got the same in AICS6 with the second artboard as a copy of the first as you've done.

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Illustrator CS6 does not save PDFs to artboard

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