It happens to me even when I am not using CL, also it happens if I click anywhere in the console, so - master bus, channels, metronome etc etc.
trying to receate it is nigh on impossible tho, it just seems to randomly happen mid project. As I said before the work arounds I have are to open the project, save it (without making any adjustments within the project) and then restart Sonar.
Another one is to change the Console view to my third monitor and have the window floating then restart Sonar.