Looks as if the flow is completely wrong, as it goes to page 1 col 1 before page 1 col 2.
You must have made it somehow so the entire document was created in a very long two column box, and the box then sliced up into pages.
I'm not sure how to use html/css for ebook pagination, so I am afraid I can't suggest the correct solution.
Is all the CSS there, I can't see anything for two column?