Shortly after posting this I found this page https://fs2crew.com/fs2crew-command-center-troubleshooting/
I checked the EXE.xml file, and it turned out that FS2Crew did not change this file (it existed from another plugin) on install. So I deleted it, uninstalled FS2Crew, installed it again + the newest beta, and a new EXE file was created with content making a lot more sense - and it's working now 🙂