If I have “Keep Quick Reference Panels on Top” turned off, open a QR panel, then turn on “Keep Quick Reference Panels on Top” it does not keep the open QR panel on top. If I close the QR panel then reopen it after changing the setting, it works. Same is true going the other way—if it’s turned on when I open the QR panel it works fine, but if I turn it off while a QR panel is open, the QR panel continues to stay on top.
New QR panels that are opened work according to the current setting. So if I open a QR panel when “Keep Quick Reference Panels on Top” is off, change it to on, and open a new QR panel, the new one will stay on top, even though the old one doesn’t.