have you ever regreased hub bearings? If so, then you should be able to check easily to see if there is some play going on.
If its not that, and possible, just put a bit more gap between rotor and pads, and yes, as already stated, check rotor trueness (do that first obviously)
Ive trued a rotor using a cleaned adjustable wrench, worked fine and not hard to true using common sense.
personally I have had this happen, and after checking the diff possibilities, just backed off the pads a bit, no more problem, and I like a brake lever that engages about half way in anyway, better for modulation imo (for my braking sytems anyway, cantis and BB7 mechanicals)