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There are only a couple reasons this might happen, by default Calibre shouldn't be screwing up em-dashes. The most likely culprit is that you have the 'transliterate unicode characters to ASCII' option enabled under 'Look and Feel' in the conversion options.
The second possibility, is more of a long shot, but maybe you have an incorrect input encoding specified - I always make a point of using UTF-8 text files instead of local encodings, but if you're using Windows 1252 make sure you tell Calibre that's your encoding - it's called cp1252 inside of Calibre. You need to go to preferences -> Plugins -> file type plugins, customize the html-to-zip plugin and enter cp1252 in that box.
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