I'm going to cover the "obvious" things (which may not be obvious?) and lets hope that there is resolution.

- The "Auto-Save" feature doesn't save constantly. It is on a timer which happens about every hour. (I'm sure a dev could give accurate times)
- You need to ensure that you don't use the Start New Game (The top option) in the parameters menu when starting the game on the server. It is defaulted to No, but.. ?
- Where ever the profile location is you need to have write access.

The way to test whether or not it is saving is to start a game, go and do something that will show persistence. Like, buy a vehicle and put it in the faction garage. (Something quick). Then, go to the Game Board (the easel) and choose "Persistent Save" A few moments later a black bar notification should come up on the right side giving the details.

Use the server command #missions to return to the menu. Start the map/game and ensure that "Start new game" isn't set, and then check.

Give that a whirl and see what happens.