Sorted, mus have been a permissions issue. Opening FLP as an administrator didn't give the issue so presumably there was no problem saving the updated setting.
This is a work PC so maybe a group policy or security settings of some sort has changed since I last changed my settings. I believe my company started doing this since the cryptolocker virus became widespread.
I know that I often have to manually copy files into the directories within the Program Files directory and can't just save from within a program not running as administrator.
However, perhaps FLP should be able to handle it a little better? Is it worth testing (if possible) to see if it's running as an administrator and suggesting it is run as administrator if not?
Is it worth me submitting a bug report in case there's any data in there worthwhile? If so, would it be from a non-admin instance?