Wow! You did a lot of tests.
I found this possible work-around:
https://askubuntu.com/questions/972276/ ... in-gnome-3
and this suggestion that it relates to gnome window manager:
https://forum.qt.io/topic/120852/make-m ... le-again/5
Did the work-around help?
Is it only this specific dialog or you do have other dialogs of FreeCAD showing this behaviour?
If other dialogs do not suffer from this issue, then I might be able to compare dialogs and "find the difference". It may be that I set some property in the dialog that I should not have...