Are you customizing your system fonts using a font management tool like Suitcase or Font Book?
This is usually a font issue. The question marks in a box appear when the font used in the document (the email may has a custom defined font that is not embedded or available via a web call) are not present/active on your machine and a suitable replacement glyph cannot be found. Usually, LastResort will fill in the blanks here. However, there are occasions, especially with old Helvetica font families, where you will see the "unknown" glyph icon.
This sounds like you have modified your fonts. You can try rebuilding your font cache. Tools like Suitcase can do this of you or use the command line tool atsutil (sudo atsutil databases -remove).
Hope this helps.