It looks like ffmpeg will not work with MOV files created using iMovie. Is there a way to batch convert these files (which are HUGE) to a compressed format, preferably mp4? I've also tried HandBrake with no success (though I assume ffmpeg is under the hood).
You may try MPEG StreamClip also. There is Batch mode — cmd+b
But it's hard to tell based on your information why Handbrake was not able to help you.
There's also Video Monkey (although it uses ffmpeg under the hood), but if HandBrake doesn't work for you, I doubt it will as well.