Just had the same problem cured in three trips to the LBS. Mine was the pedals. They weren't suspected at first because the bike only has a bout 2K miles on it. However, they were transfered to this bike from mytrade in and are actually about 5 years old. replaced 'em and now - blissful silence once again.
Bye the way - the LBS installed a cheap set of platform pedals to test the theory that it was the worn out pedals.
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Just Peddlin' Around