I'm not sure if I understand the problem correctly but will using canonical URLs help solve the problem? The gist of canonical URLs is that you let google know

I'm not sure if I understand the problem correctly but will using canonical URLs help solve the problem? The gist of canonical URLs is that you let google know there might be duplicate content, but the base url to index is your canonical URL. Quite easy to implement as well. http://www.mattcutts.com/blog/seo-advice-url-canonicalization/ http://www.mattcutts.com/blog/seo-advice-url-canonicalizatio... Hope that helps.