I'm actually seeing the same thing or at least something very similar. The source aspect ratio preference doesn't seem to 'stick' in certain circumstances.
To reproduce:
- Set source aspect ratio to 16:9
- Play a 4:3 video, it'll show up as 16:9
- Play a native 16:9 video, again shows up as 16:9
- Play a 4:3 video, it'll now show up as 4:3
- Force set ratio to 16:9 (via A or the video -> aspect ratio menu) and it'll stick again until a 16:9 ratio video is played
- Restarting VLC and playing a 4:3 video will also result in a 16:9 display, until a 16:9 video is player, that is
Seems like playing a video with a native aspect ratio that matches the source aspect ratio property puts the player into a state where it no longer forces the aspect ratio. Hadn't seen this in VLC 1.x, it's a new behavior I've seen in 2.0. Obviously this wouldn't be seen if you restarted the player between runs, but if you have videos with different aspect ratios in a single play list, this crops up.
*Edit -- Actually there's a little less rhyme or reason to it. If I hit stop on VLC and drag in a 4:3 video it'll start playing in 16:9, if I drag another 4:3 video it may or may not revert to 4:3. But again if I hit stop and drag the same video which reverted to 4:3, it'll begin playing in 16:9.