There is a lot of outdated/bad information out there on what to do for proper PCI compliance on CPanel. This is what recently worked for me:

1. In CPanel go to Main >> Service Configuration >> Apache Configuration >> Global Configuration
2. Change SSLCipherSuite to ALL:!ADH:RC4+RSA:+HIGH:+MEDIUM:-LOW:-SSLv2:-EXP:!kEDH
3. For the next 4 settings select the PCI recommended option from the drop down lists, save, rebuild configuration.

If the scan still doesn't pass CPanel's documentation site lists additional settings to check.