Missing information when creating a PDF!

Hi,
We have InDesign CS4, and I recently produced a presentation for a Client. On particular pages, I placed a jpg. of an aerial map. I then drew using the pencil tool a shape, highlighting an area on the map. I filled the shape in red and then set a transparency at 80%. This all looked fine on screen, especially when I printed hard copies out.
However, when I created a PDF of the InDesign presentation, some of the shapes did not PDF!? I don't understand why some did, and some didn't!? To get the presentation ready, I decided to create a simple elliptical shape filled in red. This didn't print out either!?
Can anyone help with this query, as it is baffling me!
Thanks,
Ajay

What PDF settings are you using? Have you tried following the directions here: Remove minor corruption by exporting

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Missing information when creating a PDF!

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