From what I have seen, the issue doesn't come from the game itself, but Steam. I have tried to run two separate game servers, both on steam, on the same box, but unfortunately Steam VAC & services port can't be changed (unless someone knows a way how) per game, so if you run one game, it will run fine, but as soon as you run a second instance on the same OS, the first game no longer shows up.
If you are running separate VM's, and you can configure them with separate public IP addresses, then it should work fine.