Another solution that might help is to look at rules containing 'font-weight' entries in the produced css - not in the @font-face rules but in general. If some are set to bold/bolder then that might explain the problems you're describing - if so either delete them or set their values to 'normal'.
It's also possible that your html contains inconvenient presentation markup (b, em, h...), although I doubt that since - in my experience - Calibre handles everything with css.
If you completely remove the css stylesheet and still have boldness problems then thats a good indicator that either the markup or - as Toxaris mentioned - inline stylesheets are to blame.
To get rid of the former you could always override the default element rendering by inserting a
Code:
b, em {font-weight: normal; font-style: normal;}
rule into your css - although that would pretty much contradict every usage of those elements, even in cases where their rendering is intended
.
For the later have a look at the html files and search for elements which contain style="..." attributes.
Finally there's always the option to convert your book using Stanza Desktop - though I would only recommend that as a fallback option since Stanza rigorously removes all presentational markup (i.e. no italics, bold, etc. anymore).