If WHM is giving you grief with this, you could manually force the ca definition into the apache config.
1) Drop the CA bundle text file into /usr/share/ssl/certs/your.domain.com.cabundle
2) Edit /etc/httpd/conf/httpd.conf
3) Locate ssl section for your domain
You should see these lines
Code:
SSLCertificateFile /usr/share/ssl/certs/your.domain.com.crt
SSLCertificateKeyFile /usr/share/ssl/private/your.domain.com.key
Add below these lines (or change the line if there):
Code:
SSLCACertificateFile /usr/share/ssl/certs/your.domain.com.cabundle
4) Save, done.
(obviously, the 'your.domain.com' should be replaced with the SSL domain cert name)