To reproduce:
- Create a Scene and set it into a Stage.
- Show the Stage.
- Replace the Stage's Scene with another Scene.

Observed behaviour:
- The first Scene reported the correct coordinates ( (3,24) in the machine where I tested this) but the new Scene wrongly reports its (x,y) coordinates as (0,0). Trying to get the absolute position of Nodes (which requires knowing the Scene's coordinates) will not work because of this issue.

Expected behaviour:
- The new Scene should report its location correctly, considering the native Window decorations.

Code to reproduce the problem can be found in the StackOverflow question regarding this issue:

http://stackoverflow.com/questions/19988580/how-to-get-the-correct-location-of-a-scene-after-it-has-been-replaced-in-the-sta