This appears to be related to the email confirmation system, not the email provider. After waiting 2 hours neither of the throwaway email accounts received confirmation emails. I then used the control panel to resend and it worked almost instantly. I'm wondering if there's a bug where the first isn't sent, and it requires a manual resend to actually work.
Since they just did all that work on severs and website etc due to the downtime it's entirely possible something got screwed up with the initial confirmation email.