Many problems with VLC are due to wrong settings or broken cache. You can solve these through deleting VLC's preferences and cache.

Reset preferences from VLC

In the preferences dialog, from the Tools menu, you can hit the "Reset preferences" button.

NB: This might not solve all your issues, all the time, then see the rest of this article.

Reset preferences and cache

If you installed VLC properly you can delete the preferences and cache by simply opening the shortcut you can find in your start menu:

All programs > VideoLAN > Reset VLC media player preferences and cache files

Open the explorer and type %APPDATA% into the address bar and hit enter. This should lead you to the AppData folder of your user.

Therein you should find a folder named vlc. Delete that folder and your done.

You have 3 options:

If you still have VLC's disk image you downloaded to install it: it includes a script called "Reset Preferences", which allows you to do exactly that. Just launch it, click OK and you're done.
If you can still launch VLC, go to the "Preferences" dialog in the VLC menu. It includes a "Reset All" button. Click it and confirm the dialog. VLC will reset and relaunch.
Alternatively, reset VLC manually by removing a folder called "org.videolan.vlc" and a file named "org.videolan.vlc.plist". Both are stored in ~/Library/Preferences - use "Go To Folder" within the Finder's "Go" menu to show this folder.

Delete the ~/.config/vlc folder or execute vlc --reset-config in a terminal.

Delete the app from SpringBoard and re-download it from the App Store to fully reset the media library and settings.