I think, it belongs to the shutter speed. I suppose you had set the camera in the "auto-mode". So far as I know, you get the best results, when your shutter speed is double the framrate of your footage. I.e. you use 30 fps, you have to set the shutter speed to 1/60 seconds. With 25 or 24 fps you have to set the shutter speed to 1/50 seconds.
To see the difference there is a youtube video from a typhoon H which had the same issues. Desperatly the video is in german, perhaps youtube generates english subtitle.
Could you please check the original video file in your SD card?
If still the same, please upload the original video file to dropbox and send me the link.