After some initial testing on real Jaguar hardware by user @pps and @BitJag over on the AtariAge forums (thanks guys!), it looks like we've got some serious issues with the particles. Which just happens to be the only part of the 3D code I wrote myself. I'm guessing the problem was that I wasn't practising good blitter hygiene. I've updated the code in question, plus made some changes to how the screen is positioned for NTSC. Let's see if that's fixed it!