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You are running the Amazon version, yes?
In version 3.3.5 (Amazon) I reordered the list of desired formats so that the amazon formats came first. I thought that I left epub enabled but at the end. Your post implies that I removed it. I can't check that right now, but if so then that is a mistake.
In any event, the fix is (almost certainly) to go to CC's folder settings, make sure epub is checked, then close the dialog. Reopen the dialog and make sure that the order of the list is what you want. My guess is that you want epub near the top.
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