The subscription has expired email has some weird issues going on with it. It looks like it's trying to send it as an HTML attachment.
I have tried this with and without HTML Email Templates plugin installed and the result is the same.
I'm still in testing mode so this is the only email that is kicked out from Pro Site plugin so I haven't been able to test the other ones. The New Site email in the Network Setting however works fine and also work perfectly with the HTML Email Templates plugin installed.
I've attached a screenshot of my settings and also what the email looks like.
Thanks for the help!