Personally, I prefer to use KVM/QEMU along with Virt Manager:
Here's also an introduction tutorial:
As for the issue with Gnome Boxes, I'm guessing that it uses KVM under the hood as well which is why it breaks. I would suggest asking about this issue in the VirtualBox forums in order to get a better understanding of why it happens and how to solve it. If anything, it might help others with the same issue.
