I had a plugin installed in Visual Studio 2008, and it created some extra dockable windows. I have uninstalled it, and I can\'t get rid of the windows it created - I close
I had similar problem except that it happened without installing any plugin. I begin to get this dialog about source control every time I open the project + tons of windows popping up and floating which I had to close one by one.

Windows -> Rest Windows Layout, fixed it for me without any problems. It does bring the default setting which I don't mind at all :)