If a window have a menubar, and the window is always on top, simply clicking the menu bar items doesn't open the corresponding popup menu, to open it you should click and drag over the item. You can easily check it by setting setAlwaysOnTop(true); in introjucer MainWindow class.
I noticed this on linux, but could be an issue also on windows too.
I think that might be fixed with the override_redirect fix I did a few months ago.
Sadly it never got merged into juce.
See http://www.juce.com/forum/topic/fix-some-issues-temporary-windows
Please try it. If it still doesn't work let me know, this is something I want to see fixed too.
OK. This is fixed for me on the latest tip. There is always a high risk in triggering some obscure bugs in some strange edge cases when changing the window ordering code - especially if it involves alwaysOnTop. So fingers crossed!
Thanx Fabian! Works great
