Windows Switcher not recognising all windows in application

I mostly use Windows Switcher in combination with Matlab. Quite often I find that it will not recognise every open window - I often try to tab from e.g. a figure to the main window but instead it just cycles through the figures never reaching the main window. If I select the main window e.g. with the mouse or regular alt tab then Windows Switcher most of the time seems to recognise if afterwards. However, using alt tab to find this window completely defeats the purpose of this otherwise excellent app. I use Windows 10.