This was discovered when trying to figure out why IconifyTest fails intermittently on Linux (see JDK-8298496).
It appears that there is an intermittent (or, on some distros, not-so-intermittent) bug when showing two stages that are both always-on-top. The expectation is that if there is more than one Stage that is always-on-top, they will be stacked in the order they were created. It seems like this isn't always the case. The IconifyTest program creates a "bottom" and a "top" stages with both set to always-on-top and expects them to be stacked in order of creation, with the most recently created Stage on top. We will fix IconfiyTest to not rely on this, but the underlying problem remains.
To reproduce this, run the attached test case.