InDesign issue with Illustrator files

Hello
I used CS3 without any issue until a few months ago.
Using CS6 on Mac now I have some problems importing Illustrator files into InDesign. When I export to pdf or jpg they became transparent or invisible.
Please take a look, this is the exported file (pdf or jpg are the same):
This is as it should be:
For the pdf I use the Gent PDF Workgroup - 2005 Specification Version 3.
Please, have you suggestion to fix this problem?

Hi, thanks all for the repies.
This is the Overprint Preview (sorry, I'm working in italian):
and these are the pdf settings
there are no spot colors, they are all CMYK.
These are the Illustrator setting
How can I check the overprinting?

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