Thanks for the details. However those options all work fine for me. Modify ePub will say no changes if it detects there is no changes to be made. Perhaps you have a duplicate in your library or something. If you still have issues PM me a link to your ePub, but I don't see any issues at the moment.
EDIT: Just saw your response - glad to hear it is now working for you. And yeah calibre always needs restarting after updating a plugin.
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