Have you checked the presence of newlines between PEM parts as suggested in the linked answer?

Also, see: https://bbs.arkos.io/t/problem-with-ssl-and-startssl/328/2

Is it possible to run the test exactly on Ajenti with the combined certificate?

Please test SSL status with https://www.ssllabs.com/ssltest/ (if your server is accessible from the web)

Does the same server+browser configuration work with a self-signed certificate generated by Ajenti?

It's a stupid question, but are you actually using a https:// URL? At least the error code suggest that you might be trying to open it with http://.

Have you checked the application's production.log for Puma errors, as I suggested?

You should see details in your application's production.log

You can either modify system (not user's) PATH on your system (no idea where and which OS you use) or just run sudo ln -s `which bundle` /usr/bin/bundle

In this case, you need to make sure that Bundler is available on default $PATH. If you e.g. use RVM and Bundler is hidden somewhere in /usr/lib..., then you can symlink it into /usr/bin and restart Ajenti.