I was having a similar problem with my customer notifications. All I would get is plain text. All the html would be stripped out. Checking the Message source showed me some messed up MIME headers.

I'm also using MIME mail with Simplenews. I tried unchecking "Use MIME mail for all messages." @ admin/settings/mimemail
and all is right with the world again.

There's some sort of incompatability with this module and Ubercart notifications.

My newsletter still seem to be working so it's "fixed" enough for me at the moment. I'm sure there's a more complete solution a PHP / Ubercart master can write. I'm not quite that masterful yet.

Hope this helps others.