If you are running the latest version of mojoPortal I have no more ideas, the reasons I stated are the only ones I can think of that would cause that problem.
If you are not running the latest version, upgrading may solve the problem. In older versions we were caching the SiteRoot as a property on SiteSettings, but this could cause problems if the site was accessible by more than one url, ie if a request came in using just the ip address the SiteRoot could get cached with just the ip address and then subsequent requests that came in using the host name would still get the cached site root from the ip address. This was changed in either the latest or a recent upgrade so that the site root is always calculated based on the current request and is not cached.
Hope that helps,
Joe