Update on this one; contacted Samsung who suggested the signal was not strong enough and that there was nothing wrong with the TV. They recommend a signal strength of anything over 80 - my TV hovers around the late 70s.
Anyway, I've cracked it and here's what I did in case it helps anyone else with the same problem (and a Google search showed that many people are having this problem due to the low signal strength of Freeview - much lower than the old analogue signal, but will increase in strength once the 'switchover' takes place).
Firstly, I reset the TV - a very simple operation.
Secondly, I found out which channels I needed to scan based on what my transmitter is outputting;
(My transmitter is Sandy Heath, so the only channels I needed to scan were channels 40, 42, 43, 45, 46 and 67).
The secret is to do a manual scan of these channels - not an auto scan. Sometimes the scan would produce no results in which case I just scanned again until it found something (which it always did eventually). I now have my full list of TV and radio stations back again.
You can work out which channel is broadcasting which TV or radio station here (useful if you're missing one or two);
Hope this helps someone!