Thanks for the replies.
It seems that a format on the device is a logical precaution - wish I'd have thought of this beforehand...
I'm tempted to see if I can recreate this problem so at least I know what is causing it. I still have a hunch about it being related to the length of the recording with it appearing in similar places on both files. I guess if I can recreate it and then eradicate it through on-device formatting then we will all be better off.