I've updated my VLC Player on the Mac and now I have two windows for one video. How can I disable this, so it works the old way?
In the VLC preferences under the Interface section check the box for Embed video in interface
When you upgrade, under the Preferences > Interface tab, you should see an option Show video within the main window. It should be checked.
If you still have multiple windows, the VLC download package has a separate app under the Goodies folder called Delete VLC Preferences.app. Run that and try again.
In the VLC preferences under the audio tab make sure visualization is set to default. This solved my problem of the visualizer window appearing on top of the video window.