The workaround from comment 8 makes matlab crash on startup.
So this is essentially unsolved without any workaround.

1 ja...@black:/tmp$ export AWT_TOOLKIT=MToolkit
0 ja...@black:/tmp$ matlab
Unable to initialize com.mathworks.mwswing.MJStartup
Fatal Error on startup: Failure loading desktop class
1 ja...@black:/tmp$

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some windows do not appear in the window list
https://bugs.launchpad.net/bugs/144406
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