@jedc768, I’ve had the same issues with failed Reply by Email emails since upgrading to Discourse v2.0.0.beta1 +4. I’ve seen rejected emails with “Email issue – Unknown To: Address” and " “Email issue – User Not Found”. I even had @nixie investigate with me and we came up empty on a root cause.
I could put together a Google doc with lots of screen shots, Mailgun error logs, and other relevant information to help figure out what’s going on. But before I do, have you discovered what’s going on with your Discourse install?