hmmm – could that possibly be the problem?
So homepage links designed to increase your PR … I think that is something GOOGLE clearly states that you should NOT do!
I believe I mentioned that nearly a year ago or more – that it was a bad idea to over do it the homepage links EG more than 10 is a really bad idea IMHO.
Maybe google picks up on the % of change in a particular page – so if a page changes more than say 52.265% its considered a new page and thus back to zero? If you had just added those links on the homepage it could be either theory at work.
In any case I do NOT think this has anything to do with duplicate content!