Are you sure that the "Save and embed" option is selected in the "Fonts" box of the "Save as eBook" dialog (see attached screenshot)?
Please click the "Exceptions..." button in the "Save as eBook" dialog. Are there any fonts checked?
Could you please email your document file (RTF, DOC, or DOCX) to
support@AtlantisWordProcessor.com?
Could you please email your current Atlantis settings to
support@AtlantisWordProcessor.com? Please choose the "Tools | Options..." menu command of Atlantis, click the "Save to File..." button, and save your current Atlantis settings as "Atlantis.ini". Please email this .ini file to
support@AtlantisWordProcessor.com.