I was getting these lines every now and then in my apache /var/log/httpd/error_log after a user submitted an order:
...malformed header from script. Bad header==?utf-8?B?R3Vlc3Q=?= <>… Use: php.fcgi, referer: http://...
The problem was that the $email address hadn’t been set earlier, and Mage/Core/Model/Email/Template.php was using a null address. This would cause the user to return to the checkout page immediately and not get a confirmation e-mail, though the order would actually be placed.
Our custom OnepageController was causing the issue by not setting the CustomerEmail in certain cases. Oops!
Live and learn I guess. Hopefully someone saves themselves a few hours with this. Or you never run into this in the first place