Oh yeah, I didn't have a server.cfg. I tested it myself after your recommendation (and to make sure my coworker hadn't made a mistake). It didn't seem to work so that was probably why.
In the end the solution I went with was to setup the mission how I wanted then run export to sqf to get a script that created the mission. I then wrote a script that removed all entities from the game (this was a little tricky but I got there.) Then I added a trigger that activated on the mission completion condition and ran both the script to clear the map and the script to create the mission. This allows the mission to replay over and over again with ever actually leaving the mission.