I'm installing Rancher on an Ubuntu server, and provisioning other servers, but when I add a SSL the CA cert goes away and everything errors. How can I fix this?

how exactly are you doing that? https://ranchermanager.docs.rancher.com/getting-started/installation-and-upgrade/resources/add-tls-secrets

I've been reading up, and I am using Docker, so I am guessing that might be the problem, but when I do add an SSL, I use the built in SSL issuer, or certbot. I think I'm going to try the recommended installation method and see if that fixes anything.

yes even for non-prod environment I no longer use docker... very easy to deploy single node rke2 or k3s cluster and then deploy rancher via helm