Many thanks for the reply. Think I may have found that accidentally! As it was a fairly recently installed system I decided to just blow away the install and start again. I had spent a fair bit of time setting the system up and didn't want to go through that again, but decided to do it anyway!
To my suprise when I started up the system for the first time afterwards I found that it had saved all my settings (although I did have to re-install a number of apps) but all my hard work remained.
If I had read your post before I did that I think I could have saved even more time as I didn't realise that running the disk and changing settings in that would transfer to my main system. So a big thank you for that.