In my experience not all html files will convert properly into pubs using Calibre and not all epubs will display on all ebook readers. I've occasionally had success in hacking the html by hand, and sometimes by cutting and pasting the text I want by hand into Sigil (open source ebook authoring software) and generating an epub from that.

However if its not happening automatically its worth stopping to work out how badly you want this thing as an epub because it can involve a lot of time and stress....