How to make mail messages use the UTF8 character encoding?
Content-Type: multipart/alternative; means that there are parts that can have their own encoding set. If your mail sending modules decide they need multipart, mail should be formatted like that:

MIME-Version: 1.0
Content-Type: multipart/alternative; boundary=boundary

--boundary
Content-Type: text/plain; charset=utf-8

This part uses UTF-8.
--boundary
Content-Type: text/plain; charset=iso-8859-1

This part uses ISO 8859-1.
--boundary--


code sample source here

If you called everything the way module docs tells you to, and UTF-8 data is not in the UTF-8 part, then you just found a bug in one of your modules.