I think I identified where the problem is. But I'm not sure.
Here it is:
I have told VLC to, say, not to show a controller in full-screen mode and/or to stop resizing player to video size. I close VLC then I start VLC Portable (portableapps.com) which runs without trouble. Close it, then when
I start standard VLC again what I see is the same alert I see when I first installed the app. As if it has reset itself back to first run status. Result: my custom settings are lost.
I know is a minor issue but it's mildly annoying at some point. Can you reproduce this on your side?
Please tell me what happens, thanks!
One more thing: settings stay the same if VLC portable is still running when I open default VLC.