Agreed, my best friend and frequent riding partner is a very talented podiatrist...he is stumped as well. however we are going to do some tests and get some scans done this season to see if we can come up with anything.
Where are you having pain? Instep (top of foot), arch or the heel? Do you where custom footbeds in your boots?
I found running in five fingers has a tendency build up connective tissue in the soles of my feet... and I need to break it up by rolling my foot on a golf ball... actually my podiatrist just got an EPAT
device that basically sends sonic pulses through your feet to break up the tissue (it zings a lot when you hit some scar tissue, but the temporary discomfort is worth it all the little bones in my feet move a lot more easily now as well as my ankle joint in general).