I suspect everything works after a full Qubes system restart? or is it permanently not working even after a restart? I have similar issues, but it's usually only happening to me when I leave my Qubes running for too long connected to a HDMI TV, or if the HDMI TV goes sleep mode on its own while Qubes is running, or if Qubes itself goes suspend/hibernate.
Everything is dodgy after returning from suspend/hibernate. Recently after newer updates (using current-testing updates here) it was enough to just restart the VM's though.
Sounds familiar, perhaps? or is your issue something else completely?