The only reason i can think that google would drop sub domains is if they were only being used to back link to the top level domain.
Like if you have 500 subdomain.domain.com sites all full of links to www.domain.com
they would drop the whole domain for being a cheater.
Google dosnt like dynamically generated pages. You could install a mod that will generate static html pages of your forum and threads, google will spider them a lot easier and you would have more chance of having entire threads showing up on google.