There is order information in the files content.opf and toc.ncx. It is done somehow with the <spine>, <guide> and the "playorder" attribute in the TOC. But, I'm not sure exactly how. I had a book that did something like what you are seeing and I fixed it. But, I have just tried some experiments, and I can't duplicate this on either the calibre viewer or my Kobo Touch.
IF I remember correctly, when I fixed the one I had, I used Sigil. I know I played with the files in a way that changed the <spine> (managed by Sigil) and regenerated the TOC. I'm not sure which fixed it.
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