I think I've found the cause of the problem. I had "video" as the capture priority. This gave perfect video on preview but appeared to (permanently) ruin the audio file on movement/noise intensive footage. Changing the priority option to "audio" gives perfect audio but faltering video on preview of similar footage. However, playback on the timeline and, more importantly, after rendering gives perfect audio AND video.
Judging by the lack of response to my original post it looks like it's a rare occurence but someone else might find a use for this solution.
I have never heard of audio & video capture priorities. I can't even imagine where i would find such a thing in this software. Can you tell us where you found those settings?
In Movie Studio, select the "Capture" icon.
This will take you to the Sony Video Capture 6.0 screen.
Select "Options" then the "Capture" page.
At the bottom is a "Master stream" option list, select "Audio".