I did not read this whole sub-thread but I do know the problem. There is a bug in the clip browser software (that apparantly can be avoided by using version 1.01) with 720/60p. I went to a shoot in San Jose and shot a whole weeks worth of interviews and had the clicking problem. Other modes do not seem to be effected such as 1080i or 1080p. My solution was to download Cineform Neo and convert all the unwrapped mpeg files in the BPAV folder. I have since purchased NEO as it does an incredible job and producing uncompressed quality video at small file sizes.
Anyway, try to steer clear of shooting 720/60p if you need the audio.