Yes the package qemu has been replaced by qemu-desktop. See this thread:
I am not experiencing this issue. Let’s see if other gnome-box users would chime in with their experience.
In the meantime you could still try this:
Open two terminal windows. In one, run journalctl -f. In the other, launch gnome-boxes and start using your VMs. Observe any error messages.
Also run sudo dmesg and look for anything related to gnome-boxes, qemu, libvirtd, etc.
Might not hurt to run a filesystem check as well. Launch your EnOS’ installer usb and run a check on your system partition.