Subdomains and themes

First, Brett- THANK YOU for your insight and guidance. I've only been in this game for a short time, and thanks to you, I'm making great strides into the big leagues. Our site languished in the mid 100's until I arrived. Less than 60 days later, after reading almost ALL of your site, and threads, we're #7 in AV, competing with the rest of the pros.
Now, a question/theory...
In examining the top ranking site under one of my terms - a very competitive one, I noticed only two pages from a subdomain. Using "more pages from this site" there were only two pages,which I analyzed. Doing a link pop check, there were other pages from the site, under the main domain pointing to those pages, but relatively "off theme". My theory is that subdomains, for purposes of thematic ranking on AV are treated as separate entities. (This is a shot in the dark, but there it is.)
I have ruled out cloaking, as the two ranking pages are not the type of pages that you would put up for the casual user vs. spider.
Link pop? Weak.. only 5. Any comments from the masses on this simplistic, statistically insignificant singular test subject sample are appreciated.