I had a similar problem with keys not working and my problem was that one of the defined key binds had a shortcut key assigned to it, with the "no pass through" option ticked, so it didn't work when VA was running. I changed the shortcut key to a shift+shortcut and affected keys were working again.
Not sure if yours is the same problem, but check the shortcuts in the bindings to see if Numlock has been allocated and change it to something else, to see if this stops the issue, then reallocate if it doesn't