I'm not a programmer, but as I understand it, it's not something support should be provided for. By raising a window on it's own, paint.net is not playing by the rules. The window manager (some windows component) should manage windows.
Also note that this isn't some weird windows addon, but a normal feature in the Ease of Access Center, called 'Activate a window by hovering over it with the mouse' in Windows 7. The same feature exists in Vista.