ANSWER:

I got this answer on my own. Actually this is a bug in VLC media player and they haven’t solved this problem till yet. This problem is caused only when playing specific file types, in my case it was .mov file.

The answer to this problem was to use different player rather then to depend on vlc. Now,whenever I want to open this type of file I use GOM player. The .mov file is played very smoothly in GOM player without opening any more extra windows.

Sad, I even tried the latest version of vlc i.e. 2.0.2 still the problem is alive.

by FrozenKing from http://superuser.com/questions/446456