If you look at your conour plot object (try a Show(obj)) you'll see that you have a list of contour plots.
When you send a message to a list, the message is sent to each item in the list. Since you're sending a save message, each item in the list is getting saved, but they are all being saved to the same file name. The last one "wins".
To save each plot as a picture, process the list of plots one at a time. Try using this loop instead of your save statement.
For( i = 1, i <= N Items(obj), i++,
name = "Wafer" || Char(i) || ".jpg"; // make a unique name for each picture
obj[i] << save picture( name, jpeg );
);