Look at the video enclosed.
This should be something like numpad with highlighted buttons that can be pressed.
Disable/enable logic of all buttons is the same: on disable we change opacity.
But sometimes buttons disappear at all rather than just change opacity.

One more strange thing showed in last few seconds of the video: when I drag some
other window over hidden component, it shows.

We do not have this issue using 2.0.3 version.
We have observed something like this in earlier versions of 2.0 (i do not remember precise version) and in version 2.1.

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It was very difficult for me to reproduce this issue in small application.
In JavaFXApplication15.rar I have tried to cut as much irrelevant code as I could.
If I cut more this issus does not reveal itself.