I experienced what I believe to be the same issue on Ubuntu 12.04 32bit with 
both ftp:// and smb:// links opened from nautilus. Both links are to my local 
password-protected NAS. I haven't encountered this problem in other programs 
yet.
I recently did a fresh install of Ubuntu 13.04 64bit, enabled universe, updated 
and installed restricted-extras. The issue perceives with VLC playing .mp3, 
.mkv h264, .avi, etc. I have not yet saved the password of the NAS in the 
keyring or added it to the bookmarks, just opened a new link, insert user/pass, 
'save only for this session', navigate to file, open with vlc which givings the 
error below, and after verify that programs like rhythmbox are able to play it.

VLC:
File reading failed:
VLC could not open the file "/run/user/.../gvfs/ftp:host=.../.../....mp3". 
(Input/output error)
Your input can't be opened:
VLC is unable to open the MRL 
'file:///run/user/.../gvfs/ftp%3Ahost%3D..../....mp3'. Check the log for 
details.

After I close the error and VLC I end up with no VLC window, just the
icon in the top menubar. I can navigate the menu and click on
play/open/hide etc, but nothing visually happens.

ps aux |grep vlc gives me:
xatr0z    8575  0.0  0.0      0     0 ?        Zl   18:27   0:01 [vlc] <defunct>
xatr0z    8994  0.0  0.0      0     0 ?        Zl   18:31   0:00 [vlc] <defunct>

sudo kill, sudo kill -9, sudo killall, sudo killall -9, sudo pkill won't
kill the zombieprocesses, the PID doesn't change.

ps axopid,comm,wchan |grep vlc gives:
 8575 vlc <defunct>   exit
 8994 vlc <defunct>   exit

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https://bugs.launchpad.net/bugs/1176379

Title:
  Streaming videos over LAN with GVFS often locks up VLC Media Player in
  Ubuntu 13.04

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