One thing is Google indexing the pages and other is to have them be listed as the most relevant for the search result. I believe you still need to let more time go by for those new pages to get their proper relevancy. This is one of those times when it is difficult to decipher the logic behind the Google Algorithm, since your home page has been in the index far earlier than those new pages it is pointing back to home page. I had a similar case with a client of mine, and eventually we got the right one. We did however get some backlinks to the newer pages. Maybe that was the defining tactic.

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I hope this helped. Cheers