Adding to the trouble of an already complex job, I went to make a mp4 with Compressor to the iPad standard as a screening deliverable and got motion stutter from footage that was the native to the Avid project.(Mac MC 5.0.3) The timeline was a mix of camera standards and frame rates - most all of it ultimately transcoded to Avid mxf media.
The Avid proj and the 'problem' footage that stuttered were 1080p/29.97 The timeline had loads of other 1080p/29.97 footage, the shots that acted up we call from the same card. The ProRes master I had output looked fine. However when I used the default Compressor preset for the iPad "H.264 1280x720 video @ 10Mbps, progressive. Audio is 44.1kHz, stereo" I got the stutter problem on clips from that card.
I know in the past I had made a copy/version of the iPad preset - where I changed the "output fields same as source" to output "progressive" For reasons I don't understand this seems to have cleared up the problem. If the default output is not progressive, why does the default setting include it in its name? "1280x720 video @ 10Mbps, progressive" You would think that playing on any computer (iPad, Mac, etc) you'd always want progressive, no?
Finally just a comment on why this can be such a 'gotcha' - you're reviewing the mp4 knowing that a lot of the footage is 23.98fps and you're bound to see less than smooth frame rate artifacts, it lowers your guard and tolerance about spotting other shots that are less than smooth. Input and ideas welcome.