You probably did this but I'll mention it anyway. My experience when I changed was that I needed to adjust saddle height and location to accommodate the changes in potitioning of my feet relative to the pedals. It may be a small thing, but it can make a big difference when riding a good deal. If you haven't done it, I suggest you reassess your bike fit in light of different shoes and pedals. It may help. Actually, the positioning of the cips on your shoes may have altered the contact point of your feet with the pedal axle as well.
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Just Peddlin' Around