After upgrading to SpamAssassin 3.0 spam is no longer being quarantined properly to the "spam" folder within the webmail. After seeing my spam levels jump I started looking for an answer.
It appears that in version 3.0 the header tag "X-Spam-Flag: YES" has been re-wored to "X-Spam-Status: Yes". This change caused procmail to simply place the spam in the inbox because no match was found. I have re-written everyone's procmail recipe and it will now quaratine based on the new match.
Individuals who are filtering spam locally using header rules should filter against "X-Spam-Status: Yes" for desired results.