Saying the key no longer works could mean several things.
With a bit of searching I don't see anyone online that has described a case where the API actually disabled the system functionality.
My first guess that the physical keys are triggering the VK_VOLUME_UP and VK_VOLUME_DOWN commands. When your app is up you get the first opportunity to handle the events Are you consuming the events in your app? Or are you passing them along to the system handlers?
My next guess is that the volume buttons might be passed along, but perhaps your system is forcing the volume levels back to the old levels frequently. I've seen cases where games inadvertently emit commands to the system ever frame, and perhaps that is what is going on here. Maybe you are setting the system volume level somewhere, so even though the user bumps the volume up your app is immediately resetting the volume.