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I have a related problem which may point to root of the issue. I too get 'spine is empty' when converting an HTML document to mobi but that's because it is, literally, empty.
Only after the coversion had failed a number of times did I notice that the original HTML document I had imported was zero bytes long in the Calibre library. There was a zip archive with a couple of ancilliary files but the actual document had not been imported.
The original imports perfectly into MobiCreator and the resultant file is no problem for Calibre.
It just looks as if Calibre won't read the HTML file at all for some reason, despite spending a fair time saying it is being added.
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