The major issue that I identified is one of the two website, the homepage/index page is having pagerank lower than the inner page. I did a backlink checked and all backlinks are going to main page, not the inner page. Question is why the inner page got better pagerank instead?
We know that pagerank from page A flow to Page B when they are linked together. And the inner page pagerank must be come from index page, as there is no external source that link to inner page.
Finally I found out from online webmaster forums, that there are few discussion about this as well. And its concluded that the same IP address is the main caused for this. Some view it as google sandbox. But its not totally correct. Google sandbox is where your website is totally drop from google SERP.
Definitely you will either need to place your websites at different web server at different location, or get a class-c ip address for each of your websites. Hostgator is offering really good seo hosting as well, view here http://www.hostgatorreview.org/hostgator/hostgator-seo/ for more information on seo hosting and how class c ip can help you as well.
