Use flatten tool with shift and Flat brush from tool's settings. But thats most probably something what you are already doing. If you really need absolutely perfectly flat area, you are going to have hard time. I know very well about that a little bit raising/lowering bug and yes, its quite annoying. It doesn't happen everytime, maybe when you click exactly on vertex, it won't occur? Just a guess. I'm afraid that this is not possible at all with current noggit version. Btw, what do you need such area for?