I also use VA and experience the same issue. I have found it depends where your mouse pointer is located when you use the voice commands.
For example I have found that if the mouse pointer is hovering over the GPS or ATC window then the voice commands do not activate in MSFS. I am not sure if it is also necessary to click on an area like the cockpit glass as well - I tend to do that out of habit.
This is an annoying ‘bug’ and it still catches me out quite frequently - but give the above a try and see if it works for you.
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