When I started with SDL2 I had exactly the same problem: my code worked in Windows but not in Linux. In my case it turned out to be because I had taken liberties with threading: I was calling SDL rendering functions from multiple threads. It should never have worked at all really, but Windows seemed to be more tolerant of my mistake.
I don’t know whether your problem stems from a similar cause, but I do notice that you are (for example) calling SDL_RenderPresent from a VLC callback, and that could well be being made from a different thread.
I don’t really know. If you un-comment the SDL_SetRenderDrawColor() statement do you get a green background, or is it still black? Do you have to use the BGR565 pixel format or can you try a different one?