I use VA as well and this is the issue. It’s a bug that’s been around for a long time. If your mouse pointer is over any open window then you can’t use any commands (keyboard shortcuts, VA commands, button presses etc.). My solution: I’m just in the habbit of always moving my mouse pointer to the floor of the aircraft when I’m done using it no matter what. I just always keep it there, near the rudder pedals. Then my commands always work. Note you don’t even need the ATC window open. Your commands will work with or without the ATC window as long as your mouse pointer is appropriately stowed 
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