I’ve seen reports that 7.0.6 sometimes does not exit cleanly and leaves kicad process hanging. That may prevent it from saving the settings correctly.
Check in task manager if kicad exits correctly.
The only one workaround I found for the time being (I was editing the thread when I spotted your answer so I prefered to comment), is to shift up the new repository.
So, instead of to have the kicad default as 1st, I have the other one. On that way it kept the repository in.
The order of repositories is not relevant, the whole config is saved the same way, if addition is not saved order would not be saved either. There is something else that is root cause.