Have you verified the the embedded fonts are actually being displayed at all (in the scenarios where certain characters aren't displaying in ADE)? One CSS syntax error could keep embedded fonts from working and wouldn't be picked up by the IDPF validator.
That would explain why the characters might display on a Kindle, but not in ADE (different system fonts with different extended character support.
Make sure your css validates.
Also note that some rare/broken fonts are not suitable for embedding and being displayed properly in ADE. There is a particular property of a font that can be problematic if it doesn't have a certain value, if I recall.
Last edited by DiapDealer; 12-14-2017 at 07:20 PM.
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