When you open an audio file from Windows Explorer with VLC, VLC will open but will skip the first second of audio and not play it. However, if you open VLC first, drag a file from Windows Explorer into VLC to play it, it will not skip the first second of audio. It seems that the skipping of the first second of audio only occurs if you open a file with VLC and VLC was not open prior to opening the audio file.
Does that make sense?