I have had this strange behavior of Sonar for some time and it is still occurs in version 2017.06.  Not a big deal but it irritates me a little.   
I save project with some tracks hidden and the console view in front, close the project and open it up again.
I expect the project would look the same as when I closed it but it is not. All the tracks are visible in the console view. I can press H to bring up the Track manager and I see the "now visible" hidden tracks do not have mark on the checkboxes so I simply press Enter and the hidden tracks are now hidden in the console view.   The track view is correct but if I bring up the console view directly after open a project the hidden tracks are visible. But if I do some small thing in track view before opening up the console view everything looks correct.
It does not matter if I have some Lense selected or "None"

Is "Keep Track/Console Visibility States in Sync" checked? That might make a difference.

The console view and track view are independent from each other, unless you do as he says above