I have flip4mac and was exporting from FCP using that.
After some more searching I came across a post on telestream’s forun regarding the same issue. Looks like it’s a bug in the most current version of the software. On the advice in this thread: https://forum.telestream.net/forum/messageview.aspx?catid=10&threadid=3603 I downgraded to an earlier build of the software and the file exported perfectly, no more strange noises.
Thanks for your response. I may still go back and test your idea on the audio and video ending on the same frame just to see if it makes any difference when I have some free time.