I get this off-and-on. Last Spring I recall this being an issue, then it eventually resolved itself, mostly after I got some cleats with a built-in varus wedge. The pain is on the outside of my right foot...same area where I had some peroneal tendonitis years ago from running. What solved that issue was going to a more flexible shoe, but I can't really do that for cycling.

Lately it's been bugging me again. I tried moving my cleats further out on my shoes. They are slightly behind the ball of my foot, too. Might there be a better placement for them?

I am riding with Sidi Dominators on my road bike, if that gives a frame of reference.