I am hoping some SEO experts can shed light on a potential problem. I have been using Google Analytics along with iFinity's URL Master and Google Analytics modules.  URL Master is redirecting all requests for "www.domain.com" to "domain.com". In Google webmaster tools I track both "www.domain.com" and "domain.com". In both instances I selected the third option under Google's "Preferred domain setting": display urls as domain.com.

I have about 15 decent backlinks that point to www.domain.com. In GA these links show up as links to my www.domain.com site. They do NOT show up as links to domain.com.

My concern is that I am losing "link juice".  Does it matter that these backlinks do not show up under my primary URL? Would I be better off in Google selecting "Don't set a preferred domain" and let URL Master take care of everything?  Any advice would be greatly appreciated.  We have been working on a number of traffic building activities and I am worried that our PR would be higher if Google associated all backlinks to domain.com.

Thanks,
Chip

Chip - I've answered this on my other post to you, but you've asked a slightly different question. To be clear : google webmaster and google analytics aren't linked at all. If you have a redirect from www.example.com to example.com set up, you shouldn't have any traffic showing up in the www.example.com analytics account. If you have got traffic, then the redirect isn't working correctly, and that might explain why things aren't working as you'd expect. The webmaster 'preferred domain' setting works by letting google know that you want to index all your site content under a particular domain. It's easier (and more accurate) to just 301 redirect all requests to the correct domain (as you have done). So this action just re-inforces your redirect. Google should update their index to match, but there is no guarantees on what the timeline on this will be.