If you are having an issue with accessing the cPanel or WHM SSL ports with Cloudflare, you may need to implement their page rules to disable caching and allow the page to work normally.
In page rules:
- The domain should be something similar to this: https://*.domain.com:2087 (the port number at the end needs to match the port you are having issues with)
- In the "Then the settings are:" Select "Cache Level"
- and set it to "Bypass" and save
You may want to set a rule for ports 2083, 2087, and port 2096 so a user is able to get to cPanel, WHM, and Webmail respectively without being cached by Cloudflare.
A free account should be able to set all of these immediately, but if you already have page rules in place, you may need to upgrade to add more.
For more information on how to do this, please refer to the Cloudflare documentation