Have you properly optimized your sub-domain? I mean to say check your website, if possible re-optimize your sub-domain with new quality content. Submit it various search engine directories. Add Google analytics code to your sub-domain and analysis your domain.
Your website is hit by Google. And your sub domain is well optimized then your main domain. Backlinks comes to your main domain have totally bad quality and mostly are no-follow with out-bound links more than 800+.
Use "Cache: " command to check when did Google crawled your homepage last time. It it says that the last crawl was about months ago then surely there is something restricting Google bot to crawl your site. Check robots.txt and fetch as Google Bot.