On Linux and as soon as we've two FXML documents opened with SceneBuilder 2.0 you cannot get the document which on the back coming to the front by calling the corresponding menu action in Window menu that basically does stage.toFront().
By Linux I mean Ubuntu 12.* and 13.* with hardware acceleration and appropriate driver. And it 's FX 8 b132.

It works fine on Windows and Mac.
Is there something specific to do on Linux ?
This issue is tracked on SceneBuilder side by the DTL-6100.

Providing a simpler test case than SceneBuilder as a whole isn't an option now, we may try to work on it later.