Hi there,
works here without a problem.
All Mixconsoles in my locked Workspaces are identical after quitting and reloading the Cubase projects.
All 3 Mixconsoles show only the chosen visible Tracks as well as the position.
Tested on Mac OSX 10.7 and Windows 8.
So did you lock your Workspaces after creating them and save the project?
Best regards,
Marcus