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Probably some naming conflict betwwen the nav and the html toc. What semantics are set on the nav? Please check that the nav property is properly set.
The best approach would be to start with a copy of the problem epub and (if copyrighted material that can't be shared, either use find and replace or a plugin to obfuscate just its text and save the problematic epub. Then privately post the epub someplace and pm me here with the location. That way I can see exactly what is causing a problem and get it fixed.
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