There is an issue with window properties, which can be reproduced with minidesk: start app1 and click on the spinning gear to show a pop-up. The first time it is shown properly in the pop-up container on the Sytem-UI side, the second time it's shown inside the app container. The logging output says:

SystemUI: onWindowReady [QtAM::WindowSurfaceQuickItem(0x16233d0)] - index: 1, appIndex: 0, type: pop-up 

the first time, and

SystemUI: onWindowReady [QtAM::WindowSurfaceQuickItem(0x1867930)] - index: 1, appIndex: 0, type: undefined"

the second time.

Means that the second time, the window property "type" is not set to "pop-up" any more.

This only happens with appman versions >= c067536 "Replace QtWayland's surface extension with a custom AM extension". Besides it only occurred with Qt5.10.1 and Qt5.11.1, but not with Qt5.9.4.