You are in the supplemental results due to the lack pagerank. Get some trusty links, not the usual spammy types one, and this should get you out of that.
Sorry I may be a bit slow. You did say content generated pages? But you also said that you had a blog on the root. Are you saying that you have content generation on this blog...or that you have content generation other than the root eg-- site/blog on folders or subdomains.
I just needed to be sure before I go on this rant here.
Normally,
I would have to know what your linking structure is like. Are you submitting these subdomains to directories or anything like that? If you are then how many subs at a time do you submit and how many subs total do you have?
Also, if you interlink from root to subdomain then there would be no need to submit the subs as the engines will naturally find the links thru the updated content of the blog.
Personally I think subdomains are a lot of work but discuss your linking structure (inbounds) and let's see if we can determine a problem and then a solution.
If your content generated pages have almost similar content then Google might believe that these add no real value to its index [ and to your site visitors ] and therefore such pages make it to the supplemental result.
Haven't visited this board often lately. Anyway, I have added some backlinks in deep directories, bookmarked them, digg a little and voila... the pages are back in the SERP. Thanks for the help guys