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That's not the behavior I noticed on my computer, and shouldn't be the intended behavior. I'm using Windows 7 and Java 7.

I'm not quite sure what you mean by this, setAlwaysOnTop will put the window above all other windows not marked as always on top, including windows from other applications. There is undefined...

1. Yes, make your windows Frameless

2. Yes, setAlwaysOnTop(boolean)