I am having this same issue.
I've included screenshots of what the settings should be, but my game.ini and usersettings.ini file do not have the info in them. As you can see in my mod config tool, the settings in my current game are not what I've tried to setup using the tool.
The things not showing in the ini files (I'm sure I don't have all of them listed here, but from what I can tell) are:
Player levels
Player engrams
Dino levels
Intervals for poop, eggs (fertilized), decay speeds for crops, crop growth, etc.
Allowable structures on platform saddles
Lastly, the mods are not being installed at all. When the server is updated, the mods folder is still empty.
If this is a problem on survivalservers end, let me know how to fix it. Otherwise, if I can get a copy of a default ini (game and usersettings) with all of the possible variables we can adjust, I can change them on my side then copy over to my server.
Whatever fixes this the fastest, please let me know asap.
My pathway for updating the changes is as follows.
1. Stop the server
2. Open the mod config tool
3. Makes adjustments as needed and click the large orange button on the bottom.
4. Wait for the server to change from orange (loading) or blue (ready)
5. Stop the server
6. Make sure the configuration is the same
7. Double check mod id numbers
8. Click large green button to update and restart the server.
9. Log in to filezilla to see if the changes were saved.
Am I missing something?
I should have much larger files when looking through FTP however, the changes (as you can see from screenshots) are not there.
I feel I would have a better time with this if you can send me a default game and usersetting ini file. I can adjust them in there (I know the values such as 0=health, I just don't know the proper wording for every variable).
I can only attach 1 file per post, I will post 3 more after this to have the other files as screenshots.
Edit: After trying to upload the GameUserSettings files to this thread, they are too large to post. I can send them to you if needed.