I have the moov atom - moved to the beginning (w/ffmpeg). No difference.
Here's what I think might be happening and also a correction on my initial post:
These mp4 videos show an error in ffmpeg (or warning), "codec frame size is not set".
If I convert to an mkv (just the container, no re-encodin using mkvtoolsnix) the video width and height are now set. If I add that to Media Center library *and* restart MC, then the resulting MKV plays back in JRemote. Is JRemote transcoding mkv files for playback in JRemote or does JRemote handle it natively?
In any case, the original MP4 plays in any other video player I've tried; only JRemote has an issue and I suspect it is due to the encoding application creating the original mp4 file and not JRemote itself which perhaps is being strict in some way other video players are not...
I have a short clip of a file I'll send to you (bob) as all of the above is barely educated guessing