Do you have the file saved with the correct name in the correct folder? It should be named mods.cfg plural, lowercase and the location is .\Steam\steamapps\common\Kenshi\data.

Also did you actually launch a game? The order is saved upon game launch, not when you open the launcher.

Shidan taught me there's also a limit of 1000 total mods, active or not, and I got this same behavior when I exceeded that limit.