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That sounds like there is an internal conflict somewhere in your fonts. Check if you have two different font files that have the same name … (I think ID takes the safe route and ignores it altogether).

If you cannot find duplicates, try deleting the Adobefnt*.lst font cache files on your system (the star stands for 'any number' — you might find more than a single file). On my Mac I find these files in my InDesign application folder, but you might want to search everywhere, just in case.

You can safely delete these files, as they will be re-built and updated on the next start of InDesign.