I have the same setup on Arch linux; 2 displays, one panel on each display, window buttons in each configured to show only windows for that monitor.
What I'm seeing is that all windows show up correctly initially, but after a while some of the buttons go missing. I have been able to pinpoint which action actually triggers the window buttons to disappear. I only notice this when it's too late already.
I have the same setup on Arch linux; 2 displays, one panel on each display, window buttons in each configured to show only windows for that monitor.
What I'm seeing is that all windows show up correctly initially, but after a while some of the buttons go missing. I have been able to pinpoint which action actually triggers the window buttons to disappear. I only notice this when it's too late already.