We think we've found a way to prevent this problem.
We found that by adding '/feed' onto the end of any post or page, you can trigger the problem manually (you will see the same feed that has been coming up random), but by adding '/feed/' on the end of the URL, the correct feed appeared. This shows there is definetly something strange going on.
With the 'FD Feedburner Plugin' you are given the option to provide the URL to two feeds to redirect to feedburner; the main feed and the comments feed.
Our previous settings only included a link to the main feed, so all calls to /feed would be redirected to the feedburner website but we did not include a link to redirect the comments feed so that would use the default functionality.
By including a link to redirect the comments feed in the settings I believe it has bypassed the method which was causing the problem (because it will overwrite the default feed functionality so that calls to /feed or /feed/ will redirect to the feedburner website).
It seems, for whatever reason, there is a bug or issue relating to the comments feeds, but by using a plugin like 'FD Feedburner Plugin' to override the default functionality, the problem is bypassed.
As far as we can tell this has solved it, though the problem probably still exists if we were to disable that plugin and revert to the default wordpress functionality for feeds.