My guess without knowing any details is that you have at 1 set of links that are common to the sites. That you have only links pointing to the front page and no deeper links. That you had decent link velocity and then stopped building links. That the links you have our directory and social bookmarks or of only 1 or 2 types.
Anchor text is a big one now also. No more than 35% of links pointing to a page should be same text. That you lack the generic links like Click here or cool site.
I would hazard a guess that its link text as that is the most common error in link building a year or so ago
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