For applications in wine (www.winehq.org), even xdotool won't work if the window is not under focus, for example run this in a terminal:
xdotool key --window wine-app-window-id --clearmodifiers Shift+Insert
But if add a sleep before, and immediately switch to the app after the command works:
sleep 2 ; xdotool key --window wine-app-window-id --clearmodifiers Shift+Insert