atlrus - 2:59 pm on May 16, 2013 (gmt 0)
In your OP you said:
We targeted a few main keywords and used an EMD matching the main keyword we targeted.
and now you say:
ink building was targeted to the specific keyword, no other links were built.
Did you use only one anchor for the links? If so, there is a chance for over-optimization, although I still don't see how the links will pass so much juice to the inner pages, if they are discounted by google, that those pages rank in the 1 SERP. If, on the other side, your home page is banned for something not link related, let's say keyword stuffing, then those links could pass full juice and google simply uses your next best page.
Of course, if I am right, adding more links could simply lead to your home page getting enough authority to overcome a page-related issue, I don't know.
Now that you got me thinking, I might pull one of those websites of mine and do the home page redo experiment myself :)