Have you used virtualization before on this system? In case you haven’t, you can see if it is enabled by checking /proc/cpuinfo:
$ grep -wo -e vmx -e svm /proc/cpuinfo
It’s possible that the virtualization options are disabled at the BIOS level, so you might have to check in there as well.
This all supposes that Boxes is actually looking for these kinds of CPU flags, etc to enable virt support and is the root cause of the issue…but I could be sending you off in the completely wrong direction.