I have a sub domain and noticed Google never reports on it in Webmaster Tools via my main domain. So I just added it as a site and it was accepted. Even further there was already some data waiting for me. Several Duplicate title and description tags I was unaware of... I'll submit a sitemap for the sub-domain to them later and see the effects. I'm almost certain it will continue to be treated as a separate site. We had also had a discussion here about Google viewing sub-domains as a Different domain about a month ago. To back this up I have started getting reports from Google that it has found my main site listed on another site (among others).. That specific site is my sub-domain. I have gotten 12 of the reports over the past day listing my site being found there on various pages. I guess the learning never ends..