If putty isn't working for you, then you can try Silicone there. It's rather permanent though.
One of the white porcelain undermount sinks that came with my granite countertops isn't quite flat enough around the drain flange area. Thus, even after I installed the drain flange with plumbers putty, a few weeks later and most of the putty has washed out in a small 1/2" area around the perimeter of the drain flange. This is allowing the sink to drain even when the stopper is supposed to be sealing it.
Does anyone have a good suggestion on how to make it seal? The "gap" beneath one part of the flange is probably about 1/16" or less.