I am creating a puppet using the original mypuppet.psd file and changing each layer with my new art. However in the character animator puppet panel I look at the mesh and is all over instead of just being over the shape of the character. I saw a tutorial telling about this problem and how to solve it by doing contour instead of auto on the mesh and after I did it , it work and I was happy .However now I have the same problem again and changing from auto to contour is not working I do not know what to do next. Any ideas.
This is usually an issue of stray marks or holes/gaps in your artwork. Turn show mesh on in the puppet panel and you should be able to see what's happening - if the triangles are extending outside of your character on certain layers, you know something extra is being included that shouldn't be.
Worst case scenario - and this has happened to me a few times - try deleting things part by part and see when it starts to work. So I might delete the head and see if the body works, then undo and delete the body to see if the head works, undo, and so on until I find the culprit.
This will be easier in the next preview 4 release - unconnected specks less than 6px will be ignored by default.