Try nesting them. The multipart/alternative content type is meant more for saying "I can show you this type of content, or this type, you decide." You're doing it right with the multipart/related to combine images with an HTML content type.

multipart/alternative
   multipart/related
      text/html
      image/gif
      whatever/else
   text/plain (a plain-text version)
[download]

If that doesn't work, I might want to see the actual output of your script, if you can reduce it to something small-ish.