When I originally wrote this, there had been an issue with the version of cPanel released. When I see people are still viewing this I believe that I should update this post.
Common issues that can cause this include IP address mismatches and missing VirtualHost entries. On to fixes:
First, check what IP your domain is resolving to here: LeafDNS
Next, from command line run /scripts/uf your-domain-name.com This is going to provide you with the VirtualHost entry for the domain. Pay attention and ensure that the IP address listed here matches the results from the bottom of your leafdns report.
Update the IP address at the registrar if that’s where you are hosting your DNS or if you’re running the DNS zones on your server, update the domains IP address from within cPanel to match the VirtualHost entry.
Normally, this is caused by the mismatched IP. Once you’ve fixed the IP address, check the site through a proxy such as proxify.org.
Below should be archived as it was fixed
with update comes woe. cPanel has set their release to version 11.25. Some sites will have problems with this where when going to the domain it will say something along the lines of unable to load template file or will just redirect you to /cgi-bin/defaultwebpage.cgi sometimes tossing a 404
cPanel says to do this:
1.) New builds, 11.25.0-CURRENT_42400 and 11.25.0-RELEASE_42400, have been published to address the issue. This issue will not be present on subsequent new installations. Upgrading a currently affected system will resolve this issue.
2.) Rebuilding the Apache configuration after the addition of the first account will permanently resolve this issue.
From the command line:
From the WHM:
Service Configuration -> Apache Configuration -> Global Configuration ->
Save -> Rebuild Configuration and Restart Apache