We got it figured out. For some reason mono was running the first server that was ever run no matter which one was executed thereafter.
apt-get purge mono-complete
apt-get autoremove
apt-get install mono-complete
Did not resolve the issue, the first server would still run no matter what.
So the temporary workaround for us was to just spin up a fresh debian vm.
Good to go!
Â
Edit: We also noticed that the cli commands don't seem to work when running the server via mono/terminal. Is there an argument I am missing? I have been running it like so:
cd /home/user/server_dir
mono "Intersect Server.exe"
Â
biosboy4's post in Portable Servers was marked as the answer