I have never seen this. I recommend to try to reset the config file.
A long time ago I tried to trace a config file bug. I tried to compare before and after states of the user.cfg file and finally gave up, because the sequence of the entries changed in a for me uncomprehensible way. It became less important, because the error I was hunting for, had vanished by other fixes. So no, I have no good idea how to trace this.