All mime parts visible in html emails

I recently installed htmlmail 6.x-2.64 and mailsystem 6.x-2.34 to replace htmlmail 6.x-1.7 on a site that uses OG to provide listservs. I had been using messaging 6.x-4.x-dev and notifications 6.x-4.x-dev with an older version of OG, but because OG no longer supports that branch of messaging and notifications I uninstalled all those modules and set everything up using og 6.x-2.4-dev, messaging 6.x-2.x-dev and notifications 6.x-2.3-dev.

Everything appears to work well except the outgoing emails. When I send a test email from htmlmail it looks good and is formatted according to the htmlmail-htmlmail-test.tpl.php file I created, and phpmailer's test email looks like the htmlmail-phpmailer-test.tpl.php.

But when OG notifications sends emails using my htmlmail-messaging-message-notifications.tpl.php template the mime parts of the message get broken. The text part and surrounding code appear at the top, then the html part, then the code of the logo at the top of the email. If I set the subscription to mail, rather than html mail, the message looks fine. I only see the html version in the email I receive. This appears to be because something in the outgoing email is interpreted as spam, at least by my ISP.

I have tried turning emogrifier on and off, I have created a new input filter to post-process the emails that only includes emogrifier, pathologic and url filters. But nothing changes the result. A subscription set for html mail messages contains all the garbage, an identical subscription set to simple mail looks like it is supposed to look.

The only other problem I encountered when installing htmlmail and mailsystem is that I can only set the theme in mailsystem to "current." If I set it to "default" or the name of the site's main theme the entire back end of the site is broken. I can view most content, but if I try to load an administrative page I get a WSOD. The only way I could fix the problem was to use phymyadmin to change the mailsystem variable back to "current."

Does anyone have a clue what is wrong here? I have attached the source for each email.