ZydoSEO - 10:53 pm on Mar 5, 2013 (gmt 0)
True, the homepages do not have any links pointing to them.
This might be part of the problem. A typical site with a natural backlink profile gets many more home page links than it does deep links.
The fact that you have links and none are home page links would raise a red flag if I were a search engine... making me question whether your backlink profile is natural or manufactured, especially if the links you have pointing to inner pages are keyword rich.