Many, many years ago reputation counted everywhere. However, we found that a lot of people were giving reputation for the posting games and so much off-topic stuff. The members on the site with the top reputation out of everyone were not even tech saavy people who were able to help others. This translated into reputation score not really being any type of measurement of helpfulness / usefulness, and it was decided that the Community Center should no longer count towards reputation.
This in part still holds true, as rep from the community forums does not count, but the posts from those forums are taken into consideration when calculating rep, which IMHO shouldn't happen because it generates crooked results.