Just to close the loop on this...
The problem is that iBooks is *very, very* picky about the epubs you use. Specifically, the content *must* be a very clean xhtml, I had issues with what I was getting for a doctype declaration. Also, the <html> tag must be right. I finally made it a standard to replace all the declarations with the ones from a new page in Sigil - and that works fine with iBooks.
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