I have the same problem, but it's been much worse lately. It bothers me before I strap into the bindings, so i don't think thats the main culprit. I have high arches, and do have custom insoles, but mainly I think, as BA mentioned, that it is because of a slight deformity in my left foot following surgery. No need for the gory details, but my pinky toe is not where it should be.
That said, can the shell of a boot be stretched? I'm hoping a slight modification in the width of the shell might alleviate the pressure and make it, at the very least, more tolerable.