I have this same problem. My startup script launches it properly, VLC hidden away in the taskbar, but the wallpaper is not centered, its off to the left a little bit. If I turn off wallpaper then re-enable it from within VLC it centers properly. The background wallpaper can also be seen on the side. I am able to still use it by making my background black so it looks fine with my particular video use, but id still rather it centered.
I use this VBS script on startup (so that no command prompt window can be seen when executing):
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Set WshShell = CreateObject("WScript.Shell")
WshShell.Run chr(34) & "C:\VLC WALLPAPER STARTUP FINAL.bat" & Chr(34), 0
Set WshShell = Nothing
with this BAT file:
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"C:\Program Files (x86)\VideoLAN\VLC\vlc.exe" --qt-system-tray --qt-start-minimized --no-audio --loop "C:\Adjutant.avi"
The settings you suggested worked to center it upon launching my VBscript.
Before and after the settings change:
All I gotta do is keep my background image black to blend with the video. I have several other options changed, like turning off displaying the video title at start of playing a video, so that it doesn't show each time the loop restarts. I have Windows 8.1 with Winstep Nexus Dock and Rainmeter Enigma skin, with this youtube video of a Starcraft Adjutant ripped in AVI format:
http://youtu.be/YEaY8One1zg