oddly enough the .mov files looks worse than the mpeg-4 and I'm working on an apple.
Just so you know, the files that are MOV or MP4 are IDENTICAL. I mean literally binary wise, exact versions of themselves. They are both the h264 coded encoded on the fly with an AVC mpeg encoder.
MOV and MP4 are containers which hold the same exact file with the h264 codec as it pertains to the Phantom.
That said, it sounds like you may have a problem with your quicktime player. And if you are having the same problem in FCPX which also uses a version of quicktime for playback (well at least FCP 7 did, not 100% on X), then your problem is with the MOV and I don't know if it's on playback or on creation. I would reinstall quicktime and that's not an easy task if you want to erase all of the prefs and residual files for it and just deleting wont do that.
If you want to troubleshoot that it's not your quicktime player that's causing the problem, PM me and I'll check it on mine and see if there is a problem. If there is not, then it's your quicktime, if there is, then it's the bird somehow corrupting your MOV files but again, there is absolutely zero difference in the MP4 and the MOV. In an MP4 or MOV container you can house an AVID Uncompressed 10 bit raw file, an animation file, a ProRes HQ 444 file, and a million others including what we have, an h264 codec.
Excuse me if I am feeding you info that you already know but the bird encodes the file on the fly and puts it on your SD card in either a MOV or MP4, again with the h264 codec.
Either before encoding or after, it sounds like you are getting a corrupt quicktime file (MOV).
Codec is short for compress/decompress. Something bad is happening to your MOV files on either the compressing or the decompressing side of things.
Send me a 3 second bit of one of your files. Send me whatever is coming out of the bird. Shoot, you will have to bring it in to QT to *TRIM it though which might be compressing it. By any chance do you have a real short clip you can send me that you don't have to bring in to FCP or QT? An MOV that is.