There is very little space available for polishing (tooling as you may call it) the disc. If you inspect it visually you'll see that the distance between the disc housing (made of iron) and surface of disc is less than 1 cm.
A good machinist will warn you when your disc cannot be polished any more (generally 2-3 polishes can be done)
The reasons for the problem you are having are anyone or all of fol :
-- Misalignment between your brake pads and disc; could be due to machining work, it happens when the lathe machine has a play or machinist has not done a superfine polishing. You can check it by simply feeling it with your hand
-- Wheel bearing requires replacement
-- At times there is not much space for polishing and removing all wavy dips, in such case a few deep ones are left out, so when you put new disc pads it takes some time for the pads to take the shape of pattern on disc (till than it will give a slight vibration)