Hey MV -
What you say here I don't think is the correct way to be thinking about it:
"My thought would have been that the sub domain is only as good as the main domain and in this case the main domain isn't strong because little or no content is hosted on it."
As I said in my original comment, there isn't really a "main domain" with a technical implementation. Your subdomain should be able to rank just fine as long as it is the canonical, has links to it, and the migration was done correctly from the old to the new. I still suspect that there are a lot of links left to the old site setup that are not yet benefitting where your site is now.
A subdomain is a separate site from another subdomain, so site.domain.com is different from www.domain.com and has its own ranking potential. Links to www.domain.com may have a knockon effect for ranking site.domain.com, but you also need links to site.domain.com to really be able to rank.
