That's odd. What is your command target set to? Does the Elite:Dangerous window have focus at all times?
It depends on the game, but some still take joystick input when focus is lost, so I'm wondering whether VA is sending input to the wrong window(possibly because another application grabs focus).
This is less likely because the physical keyboard apparently gets it working again, so unless E:D responds to keyboard input(different from virtual keypresses) by grabbing focus, it's probably something else.
If that is what's happening, your command target would have to be set to "Active Window", as explicitly targeting E:D should cause VoiceAttack to explicitly change focus to that window before sending anything.
You could test my hypothesis by running a command containing something like
Write '[Blue] {ACTIVEWINDOWTITLE}' to log
When the input commands stop working; If it doesn't output E:D's window title to the log, it confirms E:D is losing focus somehow(You could of course use TTS instead, so you can hear the window title in VR).