Join Date: Sep 2003
Location: Los Angeles
Bikes: Old Hard Rock, New Cannondale R400
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Have you checked it on a stand? If you can only feel it when you are on the bike, you might try checking to make sure your pedals or on tight. They may seem tight enough with a short wrench. You should remove them, lube the threads a bit, and really torque them up. I had a similar mystery and this worked for me. If you are only feeling it on the left pedal, start on that side.
The only reason it seems like you would feel it on the big wheel would be that you are applying more pressure to the pedal than you when you are on the granny.
I got some funny looks for this before, but I have seen it more than once.
If that is not it, next would be to check the bearings in the pedals and BB as recommended in the previous post.