Hmm discussed about in http://www.woopra.com/forums/topic/wwwor-not-to-www
I've a simmular issue, the subdomains are treated as different sites ( wich they are actually ) but we've multilangual websites, wich we want to track in one tool )
ex:
http://www.nl.domain.com ( also nl.domain.com )
http://www.us.domain.com ( also us.domain.com )
etc.
since the domains are treated as different sites, they aren't in the stats :( only the 'landing' page is ( domain.com ) where the language switch is made only ) so only tracking on the language-switch works ;-)
Sincerely,
Gerwin