Most of the shared web hosts that allow hosting of multiple sites from a single hosting account (like Hostmonster, Hostgator etc.) has a common structure. You'll have one main website or domain and all the other websites or domains will be added as Addon domains from cpanel. This way you can host multiple websites from a single hosting account. However, this approach has a problem. With each Addon domain created from cpanel, you also automatically get a subdomain (almost in all cases). Now, the challenge is to using the Addon domain, without the auto created subdomain. This may be important for your website optimization.Since, most of the times, they enable this Addon domain option in cpanel, by creating a subdomain of the main site and then pointing that subdomain to the newly created Addon domain. So in a way, the Addon domain is joined together with the subdomain, and doesn't work without it.
It's a very common problem in shared web hosts, check it out and optimize your website by implementing it!