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IIRC, when in kepub mode, Kobo changes from using WebKit for rendering to using Adobe Digital Editions. When ADE encounters anything that it can't parse, it throws away the entire file. And unfortunately, in my experience, ADE doesn't like most @ rules, including @page and @media, along with some IE-specific CSS properties like filter.
As a general rule, with the exception of @font-face, you should segregate any rules starting with @ into a separate file. That way, when (not if) ADE breaks, it will ignore only those rules and not all of your other styles.
In your case, try moving the @page rule into a second CSS file and see if the misbehavior goes away.
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