Reproducible on Linux Ubuntu 12 with default graphics shell (unity). In KDE is also reproduced but to a much smaller extent (overlapping of 2 windows is much smaller).
Netbeans project is attached. You can run it with command: java -jar <jar file from dist folder>
2 windows are created by Stage.show() for 2 different stages. The second stage is shifted horizontally by firstStage.getWidth().
When 2 application windows are created, they overlap by about 70 pixels.
With KDE overlapping is much smaller. Didn' try with Gnome.

Not a regression. Reproducible with 2.2.0 b14 and 2.2.0 b18
Not reproducible on MS Windows