You should probably do a search on "qoutes" or "qoutation marks" here in the calibre forums, as I believe this has been addressed.
The short answer, as I recall, is the encoding of the html page may not be set correctly. Therefore, during conversion, the page is being mis-interpreted. I believe the correction was to set the encoding to UTF-8 (I think), I know calibre has an option in Preferences for this.
Hope this helps.
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