I have the same problem. I have mic on usb, headphones conected to Vive (when VR is ON, then it playing in headphones), 5:1 connected to internal sound card (when VR is OFF, sound is playing on 5:1).
I turn on Voice attack, astra speaking in 5:1, when i run VR - astra speaking in headphones. When i run elite dangerous, i just hear music and sfx. Astra hear all commands, but don't respond in headphones, when i change to external 5:1 i have everything: sfx from elite + astra.
Even when i set active window in voice command to Elite (client), it didn't change anything. I think it's becouse my headphones are connected to Vive. I searched everywhere, tested every mixer setting in windows: playback, and record... don't know what to do.
ps. sorry for ma Eng.