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The process is: Input -> OEB -> Output. So every time you convert you are going from the input format to XHTML to the output fomat. Different formats suppot different things. For instance an h1 tag might be changed to a bold text paragraph because thats the closest the output format supports to an h1. The intermediate OEB is always going to be different when converting the same book between formats. That is why the xpath matches for on input format but not the other.
I don't remember the stage in the debug output the different things you listed run in off the top of my head. If no one has answered by the time I get home from work I will look and post the answer.
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