With my mouse directly in the Project window: After re-sizing the track list (shrinking the width a little bit) and the Project window (increasing it a little bit in the bottom), replacing the transport bar, saving and re-opening, CB turns back to it’s original sizes/placings. Is there something I have missed to make CB save my desired size settings?
Usually as long as don’t forget to save the project (even if you haven’t changed anything except window placement sizing etc. then it should stay in this state next time you open it (the transport bar might be an exception here - not sure).
Perhaps if you open the default project, set it up as you want then save it again as default (overwriting the original) or alternatively save as a custom template.