I'm glad that you've got partial success.
Whenever you tune a Freeview box (whether it's when you first set it up or later on), you're dependent upon the prevailing conditions for radio transmissions. (All sorts of things, from the weather to solar flares can affect the signal you receive). Also, in an ideal world you would have a different aerial for every channel. Obviously that's not possible, so your aerial is rather better at receiving some transmissions than others. (Additionally, other AB posters have suggested that ITV signals use a diffferent type of signal which makes them harder to pick up in weak signal areas).
It seems that you're probably in a fairly poor reception area (or, alternatively, you've only got a fairly simple aerial). However, your Freeview box has previously managed to lock onto a signal for the ITV channels, so it should be able to do it again.
I suggest repeating the tuning process. Ensure that you do so when it's not raining (because this can affect the signals between the transmitter and your aerial). If you don't get success on the first occasion, try again at a different time of day. (There are scientific reasons behind this but I won't bore you with the theory about the ionospheric reflection of radio waves). The signal strength required for the tuning process (i.e. for your Freeview box to 'lock onto' a particular channel) is slightly higher than is actually required for day-to-day reception. You might have to try several times but, eventually, your Freeview box should recognise all of the available channels.
Chris