Each time an account is suspended, WHM creates an .htaccess with the following information;
RedirectMatch .* http://<hostname>/suspended.page/
if server.domain.com points to the IP of WHM but domain.com points off of the server WHM is on, this is a problem. As such, the hostname needs to be updated within cPanel to something such as server.domainhostedonserver.com and then add the A record in WHM or our DNS.
After doing so, log into the server via SSH and copy the files in /usr/local/apache/htdocs/suspended.page/ to /home/<username_of_hostname>/www/ (where the 'username_of_hostname' is the username of the domain which is now the hostname) by running the command below via SSH:
cp -R /usr/local/apache/htdocs/suspended.page/ /home/username_of_hostname/www/
Chown the files to the correct user.
cd /home/<username_of_hostname>/www/ (where <username_of_hostname> is the user on the server noted above)
chown -R username.username .
Then you should un-suspend the site that was incorrectly resolving to the WHM login page and then re-suspend it. What this does is creates a new .htaccess file with the correct information in it now.