I've been running Qubes 3.1-rc2 almost exclusively, of late - and BTW, you and Joanna have done superb work in getting Whonix to work, properly, in Qubes. Thank you for that impressive Qubes effort!
On my VBox rigs, I tried upgrading the Gateway from 11 to 12, obviously, by running:
sudo apt-get update && sudo apt-get dist-upgrade
Normal 11 package updates would, of course, get installed, but 11 would never pull in the 12 package (set). Futhermore, whonixcheck would always report I was running 11.X-X.
I saw that same fail on two different fully updated OSes, both running VBox.
If you want to fix that upgrade fail, please do. In any event, I pulled the 12-releases of the Gateway and Workstation *.ova files, and both of those are running, correctly.
However, I did notice a minor issue, on both OSes. The very first time 12 is started, and you get to the 'I understand/Agreement' screen, as soon as I clicked on 'I understand/Agreement' my Gateway 12 went hard power down, immediately. On the subsequent 12 boot, all was OK, and working as expected.
You might want to find out if anyone else has seen this, and what is driving this issue, as it does not create a good first impression, especially for Whonix newbies.