After some more testing and debugging I've found the problem.

The last time I had used bibble5 I used it under Gnome and in Bibble5's
Full Screen Mode (See Menu „View” or press alt+enter).

Therefore, Bibble5 came up in fullscreen mode again when starting. And
then for some reason is not recognized by unity (at least on my 1024x600
netbook). After deleting

$HOME/.config/Bibble Labs/Bibble 5 Pro.conf

it came up in normal mode and then was working again. More or less.
Bibble5's menues also do not appear in the Unity top panel, but were
covered by the panel and thus became unavailable.

Obviously, Bibble5 somehow differs from the usual X11 programs. But
then, it was running pretty well under several Desktops like gnome, KDE,
xfce,.... It's just unity where problems occur. So I'd rather judge
unity as guilty for not beeing compatible with all X11 programs.

regards

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https://bugs.launchpad.net/bugs/779274

Title:
  Unity does not recognize a running program's window

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