When there's two of more APPLICATION_MODAL windows, only the last will behave correctly. The others would "loose" the STAY ON TOP behaviour, but not letting other windows to get interaction. This is confusing as the app looks "frozen" to a common user when the APPLICATION_MODAL window stays behind.

Steps to reproduce:
1) Run TestCase.java
2) Click the "Create APPLICATION_MODAL Alerts" button
3) Dismiss the last APPLICATION_MODAL alert (#3)
4) Dismiss the WINDOW_MODAL Alert (#2)

The primary stage will be blocked because there's alert #1 behind it which is APPLICATION_MODAL. If not, click anywhere on the primary stage.