I have a strange problem.
It seems that the VLC fullscreen controller does not auto-hide when Winamp is playing a song and using the "Modern" skin. I tried the classic skin and the new Bento skin and then the controller in VLC is able to hide itself. It is also able to hide itself if playback is paused in Winamp (using "modern").
I tried disabling as much as possible of the things that are moving around in the modern skin and closing all Winamp windows, keeping only the taskbar button or system tray icon. No go. The VLC fullscreen controller stays shown when playing music in Winamp if the modern skin is used.
Using Vista 64-bit, VLC 0.9.2, and Winamp 5.