[eluser]Ahmed Nuaman[/eluser]
Well I did some research, basically, it looks like it's a precaution to stop DoS attacks. If it sees an email with the first line of the headers starting in a number, it drops it. Many thought that for some stupid reason it didn't deliver it and just dropped it until it emerged that it was because of DoS attacks.
My main concern is why CI's emails are the ONLY emails that appear like this to my server? I've now got PHPMailer running again, and it's sending them fine, even when there's a batch of about 5400 (200 every minute).
I did do some comparing between CI's headers, newlines and compilation of the emails but I just need to sit down and really get on to this until I can find out what's causing this error.