Apostrophes dropped when flattening pdf's?

I'm using OS X 10.4.11, InDesign 4 and have tried on both Acrobat 8 and 9.
I'll make a page for a newspaper my company publishes in InDesign 4 and export it as a press quality PDF.
Because of our CTP system to go to press the pages must be flattened. When flattened we've been having issues with apostophes dropping out of the headlines. So far it has occured with Palentino and Times.
The space is there for the apostrophe but it is not visible on screne. Then when run the page through the CTP it will move the following 's' almost a tabs width out.
Is there any soloution to this other than not using said fonts?
Thanks,
Tim

Flatten the file using InDesign while exporting to PDF. Just change the PDF version to Acrobat 4 and then set the flattening to high quality. Or convert those fonts to outlines before you export to PDF.

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