Ok So I'm placing puppet tool points on a layer. Everything goes fine until I'm at about 31 or 32 points. After that when I place more the layer starts being manipulated by the points. Which is what I want but not until I have gotten them all in place.
It's unclear what you mean by "the layer starts being manipulated by the points".
Maybe it's because you have too many points and some are too close to eachother... just a shot in the dark though without more info. Maybe posting a couple of screen shots - one before the issue appears and one after- will help.