Using VLC 1.0.6 Goldeneye (Linux/Ubuntu-Lucid/Gnome)
The VLC window auto-resizing on DVD chapter change is more complex than j-b's suggested solution "force the window to not resize in preferences".
All of the time I want VLC to load a video with its actual size and so I keep 'Resize interface to video size' in preferences ticked on. Then if I wish to resize it I do. That's fine when playing a xVid/Divx/H264/Etc video regardless of container (avi/mkv/mp4/Etc) there are no auto-resize issues when PLAYING (they appear to be a DVD chapter change only problem).
But when a DVD is playing, if I resize it then VLC auto-resizes the video back to its original size on every time you reach a new chapter both when playing and when a new chapter is manually selected with buttons or menu. The apparent solution is to start a DVD playing, pause it, go to preferences, untick 'Resize interface to video size', save preferences, and resume playing the video. BUT this does not have the desired effect, the preference change is ignored until you exit VLC and restart it. So then you have to exit VLC, restart it, and load the DVD again, and remember to change the preference back again before you exit.
MKV/H264 files which have chapters encoded in them have a slightly different problem. When playing a resized video (and 'Resize interface to video size' is still ticked) when a new chapter is reached while playing then there is no auto-resize, but if you click the next or previous chapter button (or change the chapter using the 'playback' menu) then the video auto-resizes.
The situation is further complicated by the menu Video->Zoom feature (1:4, 1:2, 1:1, 2:1). These only work when 'Resize interface to video size' is ticked, so if that has been unticked and VLC restarted, to get around the DVD chapter resize problem, then you have no way of setting the video to its original size and using that as a 'image quality base' for your resizing.
The solution is two-fold:
1) Stop VLC from auto-resizing DVD and other files on chapter change, regardless of how the chapter is reached (during playback or by manually changing). Leave auto-resizing as active when a new video is loaded from a playlist (if 'Resize interface to video size' is ticked).
2) Make the Video->Zoom feature work regardless of the status of 'Resize interface to video size'.
In addition the Video menu could be enhanced with an 'Auto-Resize On/Off toggle' item, which has immediate effect (no restart necessary). This would allow users to control their video playing more easily according to their personal preference. If this also had a Hotkey, and a configurable Toolbar element then so much the better.
HTH. I should say that VLC is awesome, I love it, and this is my only gripe.