A very odd occurrence. If I type the name of my site (without the .com), a subdirectory /forum comes up before the root domain. If I type the websitename.com, then the root comes up with the subdirectory in position #2. For a while, I was partial articles from the root to my forums (subdirectory). These even included a link back to the original article at the root domain. The forum article is ranking, with the article on the root domain no where to be found. If I use a very particular, unpopular keyword phrase, the forum outranks the blog, but the blog is present. Now, I had a bunch of busted links on my blog, which I've only recently fixed. I'm not sure if this is Panda, the broken links or Google simply placing more value on the content in the subdomain. Thoughts?
you're using the terms subdirectory and subdomain interchangably, which for seo purposes, they aren't, so it's a bit tough to tell when you're asking. The situation you've described isn't that odd, if your /forum page has more links and better onpage content than your homepage does. I find this kind of thing can happen a lot for smaller sites, especially since a lot of people don't put a lot of content on their homepages. I wouldn't worry about it too much, as the sites ages and develops things will straighten itself out. If it really bothers you, build a few links to the homepage with the url as the anchor, and it'll outrank for the branded search in no time
Though I agree with BCRed that you need to be precise but your answer can be that subdomain/sub directory is getting more traffic/backlinks than your main page. Google ranks pages within site based on following factors: 1) Keywords Searched 2) Relevancy 3) Authority My suggestion would be to build more backlinks to main page.