Permission on the server can get out off whack because of uploading files the wrong way, transferring to another server, you name it. Unluckily there are several exploits that make use of this. So checking and fixing file and directory permissions is a good place to start when something is wrong. For Magento 1.9 (if…

So you updated to Exim 4. Great. Are you using a relay server like Mailgun, Mailjet, Sendgrid, Mandrill, Mailget Bolt, SendPulse or Mailget SMTP? Chances are that emails send to your own domain are not getting through. You will get something like this (Mailgun example):