I usually use the SMTP module for D7 to send e-mails with a relay. This stopped working on one site after changing the relay configuration. All mails were sent through the standard Drupal mail system, although the module was active. The resulting e-mails had a user agent of "Drupal" instead of "PHPMailer". By looking at the install script of the module I found that in the mail_system variable there should be a key-value pair of "default-system" "SmtpMailSystem". Instead, the value was "DefaultMailSystem". Changing it to "SmtpMailSystem" made the module working again. It's not clear why this configuration changed and does not change back if the module is explicitly activated. Maybe there is a compatibility issue with Maillog which also writes a key-value pair in this system variable.