ZydoSEO - 1:37 am on Oct 3, 2012 (gmt 0)
Hopefully you're not "fowarding" the www to the non-www version of the URL (BTW... BOTH should likely be http except for any pages that need a secure connection like checkouts or forms requesting sensitive information).
If your canonical or prefered version of the home page URL is http://example.com/ then you should be 301 redirecting all requests for http://www.example.com/* to http://example.com/*.
If you request http://www.example.com/ and that request returns anything other than a 301 Moved Permanently HTTP Status then your http://example.com/ URL is likely not getting credit for the link (unless you have a canonical link element in the <head> of http://www.example.com/ pointing to http://example.com/).