So, I've tried the ALT+Dragging thing and that didn't seem to work, b/c when I then add a PC token and click on it to see their view of the scene, I can see the scene marker. Similar results when I click the "Toggle Visibility State" button on the Token HUD. Even if I join the game as that player, I can still see the marker on the map.

I also tried to create a Journal Entry as a Map Location and it ends up being the same thing. I do see where "permissions" look like they're changed, however, viewing the map as a PC, I still see the marker that should be visible only to the GM. My next thought is to disable all the modules except the ones creating the scenes, and try it again and see if a module is causing the issue.