Callus under the ball of my foot keeps coming back

I run three or four times a week and I have a callus under the ball of my right foot, roughly under the joint of the big toe, that will not stay gone. I file it down every couple of weeks, it goes smooth, and within about ten days it is back and slightly annoyed about it.

The left foot has nothing at all, which is what puzzles me. Same socks, same shoes, same routes. It does not exactly hurt, but I am aware of it when I am barefoot on a hard floor.

Am I doing the filing wrong, or is there something else going on that filing will never fix? I would rather understand it than keep sanding the same spot forever.