The configure windows(only PL secondary windows) will be lost focus by the yellow highlight(which showing what process name is being restraint at that yellow highlight) when you move the mouse to there, which focusing a configure windows that don't force the focus.
Except "ProBalance Settings", as you can't click the main window after you open it. :)
The issue here is actually that most of the configuration dialogs did not have the main window set as their parent. This is now fixed internally.