I think I understand just what you are saying, I have a hosted account like this as well, but I'm not trying to get mine to be SEO friendly.
I can see how if the secondary domains are related to your main domain through the subdomain access URLs. Do you know if your host gives you the ability to disable this subdomain that is created for the shared accounts? This is where you should start, I think it would be best to have domains and subdomains that pertain to the particular site only. I'm not an SEO expert by any means but I do see how the content of your domain may be confused if the sub domains like this are being indexed along with your main domain.
Anyone else out here in the forums have any experience with this?