Tigermom does have a good point--you might have a leg-length discrepancy (many people do) that doesn't matter on flat pedals, but causes problems clipped in. (My fitter put a shim in either my shoe or cleat (can't remember) to help with that).
I think if it's causing enough pain that you can't ride and are having a hard time walking, it's well worth the drive to do another fitting. It's cheaper than the conseqences.