If you happen to be following the Rails Recipes for this, I ran into trouble until changing the name of the file from "multipart_alternative.rhtml" to "multipart_alternative_html.rhtml". There seemed to be a conflict between the content_type "multipart/alternative" and the file-name-based magic of setting the content type.
I think you can change the name to anything other than "multipart_alternative.rhtml" and get the same results.
Look at the generated email and see if the HTML part is given a MIME type of "text/html" or "multipart/alternative". (I dealt with this months ago and don't recall any more specifics.)