This behavior I noticed on my multi screen setup. In the Window button menu I have set the "Active window is maximized" option. This works fine while you have only one screen. But if you have multiple screens, you will have the problems, that if you have two maximized windows, one on each screen, and you change the active maximized window, the window buttons on the other screen will disappear (because no window on this screen active anymore). I think I already pointed out something similar in an earlier issue opened by me, where you suggested to switch to a latte panel (which I am still using). The better way would imho be to keep showing the window buttons for the last active maximized window for each screen.
This behavior I noticed on my multi screen setup. In the Window button menu I have set the "Active window is maximized" option. This works fine while you have only one screen. But if you have multiple screens, you will have the problems, that if you have two maximized windows, one on each screen, and you change the active maximized window, the window buttons on the other screen will disappear (because no window on this screen active anymore). I think I already pointed out something similar in an earlier issue opened by me, where you suggested to switch to a latte panel (which I am still using). The better way would imho be to keep showing the window buttons for the last active maximized window for each screen.