I am implementing a Single instance process pattern on Windows.
When a process instance starts,it does contact the running instance and asks it to push an FX Stage to front (Stage.toFront()). When doing so, the Stage is moved on top of any FX Stage of the running instance, but is not moved on top of any Window.
I emulated in the attached testcase the inter-process communication with a timeline that makes the Stage labeled "Scene 1" to be put on top.
Run the testcase, 2 stages are displayed, after 10 sec, the stage 1 is asked to be moved to front. You will observe that it is moved on top of stage 2, but not on top of any window you could have put on top.