I'm fairly new to the S1 but I experience the same issue here...I did know this and it's not quite the problem I'm having. Rather when I move to a different track in the main window and then come back, the visible CC lanes/velocity have changed. And it's not that it retains the order of the track I was just looking at. It just goes to some kind of default. (It doesn't happen all the time.) I also don't know an easy way to recall the configuration to get the lanes back other than to reselect them with clicks. Also there clearly could be global automation lane presets if Presonus wanted to institute them. An instrument may not use them, but what does it matter if there is an unused CC11 lane? How is that any different than an unused pitchbend lane? And the process of adding a CC lane is convoluted, requiring pop-up box and several clicks.
Correct me if I'm wrong but you are referring to the problem related to the configuration of the Event Automation Lanes (Lane) within a given Instrument Part in the Edit Window, I believe.
By default for each Lane S1 offers Velocity, Modulation, Pitch Bend, After Touch as Parameters. Based on your needs and the offered Parameters by the assigned Instrument (via the Instrument Track) to be automated, you can add additional Parameters to the Lanes. In order to view/edit multiple Parameters at once you need to create multiple instances of Lanes and select the relevant Parameter for each Lane separately.
Issue: for whatever reason, whatever you set up, S1 does not persist correctly the selected state of the Parameters in the Lanes. Whenever you e.g. add a new Instrument Track or even sometimes just change the selection of an Instrument Part/Instrument Track, S1 falls back some default Parameter selection across all the Instrument Tracks i.e. you can start the selection exercise from the scratch.
Do I miss something?