I don't know the solution. I've experienced this with some files from a friend of mine. They play perfectly in Windows Mediaplayer but do nothing in VLC. This is the first time ever that it's not the other way around. This is on Windows 7.
Are there any updates on this issue with mov-files spawning new vlc windows outside of the navigation window? I'm on vista business 32bit with vlc 0.8.6.i janus, default settings, ati graphics driver, dual monitors. It occurs when i use "Open directory" or select a couple of podcasts.