The new version (.9.4) is still canceling your selected zoom setting at the start of every clip. The old VLC (.8.whatever) would do this when the files in the playlist differed in size, but the new one does it even when repeating a single clip.
If you set the video to double size, for example, it should STAY there until you change it.
It seems like such an easy bug to fix, and it's such a major pain in the can...