ok,
Windows7 64bit
Paint.NET v3.5.10 (Final Release build 3.510.4297.28964)
1.open Paint.NET
2create new project with File > New on top bar
3.zoom it until right and under scroll bar appear
4.scroll both bar to change position without 0,0
5.move cursor over windows(History,Layers,Tools)
6.position will be automatically reset to 0,0,in other words.,under bar will be set extreme left and right bar will be top.
If automatic reset position doesn't occur then try to use mouse wheel.