EPUB export is only available as "Formatted Text" or "Plain Text". If you take a look at the explanation in the User's Guide, page 24:
http://www.abbyy.com/fr11guide_en.pdf
Quote:
[...]
c. Formatted Text
Retains fonts, font sizes, and paragraphs, but does not retain the exact spacing or locations of the objects on the page. The text produced will be left–aligned. Texts in right–to–left scripts will be right–aligned.
Note: Vertical texts will be changed to horizontal in this mode.
d. Plain Text
This mode does not retain text formatting.
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Although that is a slight lie, the EPUB export strips out even the fonts/font sizes to make even cleaner code.
If you wanted more complex formatting to be carried over, you would have to export to one of the formats supported in "Exact Copy", "Editable Copy", or you can take a shot at trying to clean up the HTML Exported by using "Flexible Copy" (although let me tell you, the HTML is UGLY).