How do I REALLY reset the Visual Studio window layout?

Have you tried this? In Visual Studio go to Tools > Import and Export Settings > Reset all settings

Be sure you back up your settings before you do this. I made the mistake of trying this to fix an issue and didn't realize it would undo all my appearance settings and toolbars as well. Took a lot of time to get back to the way I like things.

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 :)

Try devenv.exe /resetuserdata. I think it's more aggressive than the Tools > Import and Export options suggested.

Also check Tools > Add In Manager and make sure there aren't any orphans there.

How about running the following from command line,

Devenv.exe /ResetSettings

You could also save those settings in to a file, like so,

Devenv.exe /ResetSettings "C:\My Files\MySettings.vssettings"

The /ResetSettings switch, Restores Visual Studio default settings. Optionally resets the settings to the specified .vssettings file.

MSDN link