domain.com and
www.domain.com are treated as two different hosts with different index urls by Google, and thus have their own backlinks and PR... you need to try and aggregate all your incoming links (both internal and external) to one url - ie. usually
http://www.domain.com/ with a trailing slash, so apache will serve the correct index page.
It will only affect your serps in that you are not competing with the full weight of all your pagerank if the PR is split between www and non-www versions.