Google Analytics setDomain beware

In May I added a google analytic line of code that should be used when tracking users among different subdomain under the same profile. The call in question is setDomain. I went through the documented steps (http://code.google.com/apis/analytics/docs/tracking/gaTrackingSite.html#domainSubDomains) and pushed it to production. I have used this functionality successfully previously. About a month later I realized that...