I recently had someone ask me why their windows seem to shift around when they go from Design to Debug mode. The answer is simple: Window Layouts. You may have seen them if you have ever tried to export your settings. It can be found under General Settings -> Window Layouts:
There are, in fact, four Window Layout modes in Visual Studio:
Design View - this view is the one you see when you start up Visual Studio. It's what most people refer to as the "normal" view.
Debugging View - this is the view that you get when you enter Debug Mode like when you are stepping through your code.
Full Screen - the view you get when you go to View -> Full Screen (SHIFT + ALT + ENTER).
File View - the lesser known view you can get when you open up a file via DevEnv.exe [filename]The
The thing to remember here is that, both, your tool windows and your command bar customizations are saved separately for each state. There is no way to tell Visual Studio to use one state for all modes at this time. Additionally, when you shut down Visual Studio in any state, all four states are saved.