This sounds like an issue loading the needed VLCj files. Not only are dlls required but the plugin directory is also required. As the execution location moves around from inside eclipse to back in the file system, the path to these files may be getting set incorrectly.
It sounds like you have it working within eclipse. This would indicate to me that what you have should work. Firstly, I would recommend acquiring the VLC dlls, etc., by providing this as a VM argument such as shown below, rather that setting it in code. Remember to comment out any loading you are doing in your code so that you are relying on the command line argument.
-Djna.library.path={Application Location}/lib
example: -Djna.library.path=C:/myapp/lib
Directory Contents:
lib
-- libblc.dll
-- libvlc5.dll
-- {etc}
/plugins
/3dnow
/access
{etc}
If you are still having issues, add the following argument to put VLCj into debug mode. This can be very helpful to determine where things are failing.
-Dvlcj.log=DEBUG
Hope that helps.