Hugh,
I was just grappling with this issue myself and stumbled upon a solution. For me, it was as simple as going into the Log and Transfer settings dialog and changing the VIDEO format to Apple Intermediate. I also have the audio set to plain stereo, so it could be just the right combination.
Couldn’t find this advice anywhere else; I heard a lot of “Set the audio to plain stereo” and didn’t have any luck. Now I’m logging and transferring like there’s no tomorrow! Thought I’d share for anyone else having problems.