Hi, @RyanMG. Without seeing the PEM files myself, my answers are only best guesses because I’d need to see the actual files to say for sure.
With that caveat, it sounds like the Cloudflare Origin RSA PEM certificate is not the intermediate or chain certificates required. That or it is in the wrong format.
It might be helpful to send me copies of those files to examine. Now, if you share the actual PEM files with me, they should no longer be considered secure and you would need to revoke them and generate new ones. However, sharing them would likely allow me to test them so I can tell you what files to use or else what isn’t working.
Would you be willing to private message (PM) the file contents to me? I’ve confirmed private messaging is enabled. Likewise, if you do plan on revoking the certificate and issuing a new one (and I strongly recommend that you do so), you might just post the actual files here. If you are revoking them anyway, sharing them isn’t going to be a security risk as you won’t ever use that SSL certificate for the site. If you do this, it will also provide a real world example of the Cloudflare certificate and key files to help the next person that runs into this.
So, either via PM or posting publicly, would you be willing to share those files with us?