I can only assume that you implemented the code changes as well as friendly urls and now Google is re-indexing your site. So that can take quite some time.
In the meantime you will have a lot of duplication till it settles down.
It could take a very very long time.(Weeks,Months)
Unless possibly you resubmit a sitemap(Giz hack)

Probably something Giz and Id242 should have mentioned.

Blue Man Group
There is no such thing as stupid questions. Just stupid answers