It appears that the position values (top & left) are being reversed in the registry when Paint.net is closed. Or it's reading top for left and vice-versa when it opens.
For example, if I edit the registry and set both values to the same number, such as top:10 and left:10, then Paint.net positions correctly when I open it.
If I move the window to position top:10 and left:400 on my display, then close and re-open Paint.net, the window positions to top:400 and left:10.
I have version 2.72 installed.
