However, if I make a change on the test site (e.g. make the board inactive or change the inactive board message) then it affects our live site. Some things are affecting our live site (for example if I make changes to notices but some things are not such as Chris's notifications).
I'm confirmed that the test install is set correctly in the config.php file to use the copy of the database, not the live one.
The only thing I can think of is that as we have a CDN on our live site that somehow cached something and is affecting things. I've asked our hosts to clear the CDN cache.
Any other ideas?