This is a problem for me too. I wanted to use VLC to display demo clips on a screen in a perpetual loop, but it just looks too unprofessional when the player pops up on the screen between each clip, regardless of what the background looks like.
Perhaps it would be possible to lock the view to a set window size or fullscreen, regardless of the video clip? Then VLC should stretch/shrink/letterbox all clips to fit the selected window, without changing any graphics settings. That is in essence what I have done anyway, it's just that VLC forgets this between clips.
This is useful in multihead setups also. It's an annoyance when the video keeps popping up on the "wrong" screen.
(PS, anyone have suggestions for a good alternative to VLC for my use? QuickTime doesn't load more than one file. WMP doesn't get the file formats, and if I have to transcode all the clips, I may as well edit them all together to one clip, but neither is a very flexible solution for me. I'm on Windows.)