Cannot extract the embedded font"...". Some characters may not display or print co

Been trying to find a solution for this problem that has been rearing its ugly head for years now...
Its definitely related to flattening transparencies, I believe, as it only appears after I click 'APPLY' under the apply to pdf section of the Flattener Preview Dialog.
Im exporting the files as pdfs(interactive) from CS6 Indesign. I then have to flatten the transparencies for the digital addition requirements while leaving the fonts embedded. No problems until I try to Flatten the transparencies. Several files return the same error for a number of fonts.
I've read that could be specific character issues. Font Doctor finds no issues with the fonts in question.
Also getting a similar error regarding character widths.
Others have reinstalled the fonts to no avail.
Does anyone no of a workaround that doesnt require using alternate fonts?
Ive dumped the font cache too. Didnt help.
Thanks for any advice in advance,
KMH

Just to let you know, for anyone else with this problem. I had this problem occur on a MAC when you tried to do save to PDF in excel. This was all happening at the point of generation of the PDF in my case.
The fix was to delete ALL the microsoft preferences, but perahps only the font cache needed to be deleted.
I deleted the following areas from the local users userprofile on the mac. On windows, I would probably log in as a differnet user to try to see if the problem just exsists for one particular user.
Here are the sections I deleted:
Library/caches/metadata/Microsoft*
Username/library/preferences/com.microsoft* ( and anyhting with microsoft in it)
I did leave the entourage settings though.
hope it helps someone with a similar issue.

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    Just to let you know, for anyone else with this problem. I had this problem occur on a MAC when you tried to do save to PDF in excel. This was all happening at the point of generation of the PDF in my case.
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    I deleted the following areas from the local users userprofile on the mac. On windows, I would probably log in as a differnet user to try to see if the problem just exsists for one particular user.
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    Username/library/preferences/com.microsoft* ( and anyhting with microsoft in it)
    I did leave the entourage settings though.
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    Just to let you know, for anyone else with this problem. I had this problem occur on a MAC when you tried to do save to PDF in excel. This was all happening at the point of generation of the PDF in my case.
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