Originally Posted by Koyote

That suggests the problem may be with the caliper. Have you got another caliper that you can try, just for comparison?

It may not even be the machining on the caliper mount. Perhaps the brake pad isn't seating fully in the caliper. Pull the brake pad from the front, and try it in the rear. Make sure it's shoved all the way into the caliper.

I'd try all of the above before taking more drastic measures like milling down some part.

If the problem IS with the frame - which is unlikely - you need a shop with the correct tool to face the brake mount.