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That's a really complicated workaround - Calibre should be able to convert the html/pdf directly. Not sure how you're adding the books - pdf should never wind up as a zipped file in Calibre. HTML will be converted by Calibre to a zip file so all the related html files can be held together. As long as Calibre zipped it and you didn't zip it yourself you should be ok. Try adding the books by dragging'n'dropping the files from explorer/finder to Calibre's book list.
If you've imported the books correctly and you're still having a problem then we would need to see the error messages you received during conversion to help you - alternatively you can just post a sample with the error messages to bugs.calibre-ebook.com.
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