I guess it is failing here (not sure): https://github.com/pkp/pkp-lib/blob/master/classes/mail/SubmissionMailTemplate.inc.php#L67
But that is the only way I can think of using the hook here https://github.com/pkp/pkp-lib/blob/master/classes/mail/Mail.inc.php#L463
@asmecher any idea why using that hook to send mail with a plugin like https://github.com/ajnyga/useGlobalSender/blob/master/UseGlobalSenderPlugin.inc.php#L72 would stop the email logging from working? That can not be intended?
We have used a modified version of the core with basically the same changes since December and the email log does work for us, so probably the problem is with the hook (or the way the plugin is using it). I suggest that you switch the plugin off and wait for the changes to the core. As I mentioned above, I have not tested it much.
edit: I will add the same disclaimer to the plugin readme, but will leave the plugin there, because I think it is the only plugin available that shows how to use you own mailer code.