There's a calibre plugin called ScrambleEbook that can be used to get help with copyrighted books. It garbles the text but leaves all formatting in place, so no copyright is being violated. It's been approved by the MobileRead Editors/Moderators for exactly this type of use.
If you could share the scrambled epub, that may help someone diagnose the issue.
The ScrambleEbook plugin can be found
here.