A poster on the UP board has been keeping extremely detailed accounts of the RPI as it related to women's soccer. Check out his incredible website here:
You can wade through all his data, but in short, he proves that the RPI is completely biased against West Coast teams, primarly because of the fewer number of "inter-regional" games West Coast teams can play due to geographical and cost issues:
According to his calculation, in women's soccer (which I believe uses a very similar formula to baseball), a team from the West is penalized an average of nearly .04 points (very significant).