Irony of ironies...
I've just replaced our old rear-projection/LCD television with a new, larger LED/LCD and all of a sudden I've got this judder problem on DEEP SPACE NINE. I messed with motion control settings until I was blue in the face, and no matter what I did, every time there was an outer-space scene, or a scene with credits or any other form of video processing, like phaser blasts, Odo morphing, whatever, the motion would get all jerky-looking.
So, like a good soldier I referred to the Internet, put "DS9 Jerky motion" in the search engine, and it led me to this thread - and I was the last poster in it! My advice from two years ago was fine for my universe at the time, but in truth, the answer I was looking for was earlier in the thread.
I too have a Sony Blu-ray player and I went in, shut off the BD-DVD-ROM 1080p setting and all was fine. This is great - I was looking into using an older DVD player just to run my DS9 discs, but this has fixed it. Thanks to all upthread for the answer.