I have a problem with pain in my big toes, mainly worse in my right foot rather than left. Becuase the pain wasn't acute, and was kind of dull and annoying, i waited for a while to get a diagnosis.
I wear motion control shoes too (Kayano) and recently went to see a podiatrist, although the shoes are stopping the pronation, both my big toes were 'impinged' at the joint. This meant that instead of the normal pronation that occurs with running and then push off with the big toe, I was pushing off the joint under the big toe.
I had orthotics made to release the pressure on that toe joint.
So far they've been great.