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Hi,
I do not think that this is the problem.
Normally this happens if the file itself is damaged or has some really strange codec.
I had some videos which opened about 20 windows with VLC but only one in Windows Media Plyer classic.
Broken files can also cause this. And other players don't have option to playback multiple video tracks at the same time, so they won't show the issue.
Windows Media Stream Editor should work for removing unneeded stuff (demux and create new file).
I'm experiencing the same thing on a number of wmv files I downloaded in an archive, and re-encoding them all is going to take a significant amount of time I don't want. Is there a setting to turn off multiple playback windows and only choose the one with the highest quality video?
Windows Media Stream Editor. You don't have to encode anything, remuxing is enough. There is also feature request for VLC. http://trac.videolan.org/vlc/ticket/2407