I have this problem where I open Visual Studio and the internal windows are scattered all over the place. None of them are docked; some that should be visible have become in
My issue is similar, but the result is the app crashes. The problem was this value
In HKEY_CURRENT_USER\Software\Microsoft\VisualStudio\11.0\MainWindow. It was set to "0 1000 -280 -100 3" probably due to having multiple screens and moving the UI around a lot.
Deleting this value allowed the app to restart successfully. It gets recreated on startup.