Differential foot stress?
Perfect pedaling is actually on the rare side and generally takes a lot of work to develop.  That being said many people pedal in an unbalanced way (I tend to have a much stronger downstroke on my right and upstroke on my left).  I use clipless however, so my feet are always in the proper position (for me).  If your foot position varies or isn't correct (for you) you may experience uneven pain.  It's also possible you have an unbalanced stroke.  Either of these could contribute to single sided pain.