Wacky brush pivot points

Maybe I'm just not understanding how it works, but most of my brushes' pivot points are really far away from the actual brushes. when I create a new cube or new cylinder or whatever, the pivot point is in the centroid of it as it should be. But somehow with the cloning and moving around and everything that I do, the pivot points run away. When I click "reset selected pivot points", sometimes they get closer to the actual brush, but sometimes they go even farther away. It seems like a bug to me.

I noticed something today that may be part of it. when I press "T" to "size bounds" I noticed that, when I moved one red dot (x axis boundary) inward (to the right), the pivot point moved to the right as I was dragging it. When I then moved the other red dot inward (to the left), the pivot point moved to the right also - farther away from the box.