It was captured live from the camera's 1080p SDI output with a recently-purchased Blackmagic Mini Recorder in ProRes 422. I sent the clip to Blackmagic tech support, and they confirmed they can see the stuttering, but said they've never seen such a thing before and have no explanation for it.
There were no dropped frames during capture, and when I step through it frame by frame in FCP, it looks fine to me. So on the surface it looks like there's no problem with the file.
But during playback in FCP or QT Player, it jumps, stutters, or "snags" at particular points in the footage. But not always at exactly the same frames, and only sometimes - If I play it in a loop, sometimes it plays perfectly smoothly. I tried playing it on several different fast computers, eg. 8-core 2.26 GHz Mac Pro with 180MB/s drive, so it also seems like playback hardware speed isn't a problem either.
I tried converting it to uncompressed and playing it from a RAM drive. I made an H.264. I even output it as a TIFF sequence, all the frames looked fine but when I reassemble them again into a movie, it still stutters... I can't figure it out!
Are there any tricks I can do in FCP to smooth it out? Any diagnostic tools I could use?
Have you tried trashing your FCP preferences? This did the trick for me when I was experiencing the same issue. It's in your Users/Library/Preferences folders. Trash them then restart Final Cut. Hope this helps!