Run the code.
You can press left button to change the pref size. and mouse click to change TOP and BOTTOM alignment.

Press left several times (3+), click with mouse on scene.

Clicking mouse and pressing left (many times, between clicks), you can see, that pref size affects only after changing alignment.

Affected tests:
graphics/api/control/separator/SeparatorTest1Test.java
graphics/api/control/separator/SeparatorTest2Test.java