If the signal strength at your house isn't particularly strong, your Freeview box won't necessarily be able to 'lock onto' all of the available 'multiplexes' (= 'bundles of channels') in a single scan.
If, like my own Freeview box, there are separate options for 'Replace channels' and 'Add channels', you might need to do an initial scan using 'Replace channels' and then another one using 'Add channels'. (Actually, to get all available channels, you might need to do an 'Add channels' scan several times after the initial 'Replace channels' one. I usually need to do that).
If you've not got separate 'Replace' and 'Add' options available, you could try recanning repeatedly until everything locks into place. Ideally, perform your scans early in the morning with your computer and monitor turned off (because there's less chance of your neighbours having similar equipment turned on at that time), as all electronic equipment generates signals which can interfere with a scan.