On reviewing Start11, I see that it does not work on the tray icons. It was WinAero Tweaker which did that for me. On checking the registry value, I see that the number of tray icon rows did not get reset from 2. I even used WinAero Tweaker to set the number of rows to 3 and restarted explorer, but I still have only a single row. I think DrJBHL was correct that it was the Windows update that caused the problem. Nothing to do with Start11.
