forums fall victim to this alot, it is called split PR. Alot of forums are under domains and the main amount of traffic goes to the domain, yet the forum scripts link to index.php.
Example:
http://www.LinkinParkForums.com and
http://www.LinkinParkForums.com/index.php are considered different pages with PR. I modded my forum to prvent this be sending all the index.php links to just / that way almost all of my traffic goes to / not index.php