Something worth trying is embedding the fonts into the epub file. I recently made an epub which had italic words using <i></i> tags. When I opened the epub in Adobe Digital Editions (God how I hate ADE, all hail Calibre) without the embedded fonts it ignore the italic tags and the words appeared in regular font. After embedding the fonts ADE read the italic tags perfectly.
I'm not sure on this, but my problem at the very least seemed to be down to ADE's really wonky support for tags within epub2 files (small caps also aren't supported). Yet when I converted to epub3, even without embedding fonts it worked fine.
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