If just one channel is missing, you might be able to get it back by re-scanning your Freeview box. (If you're offered the opportunity to choose between 'adding' channels or 'replacing' them, choose 'replace'. This forces the box to 'start from new' and is more likely to fix the problem).
If that doesn't fix the problem, it might be due to insufficient signal strength. Even though both boxes probably take their feed from the same aerial, the quality of the cabling to one box might not be as good as to the other one. (Or, of course, one cable could simply be longer than the other one. Either way, there could be greater signal loss in one cable than the other). Additionally, some Freeview boxes have a greater 'sensitivity' (i.e. ability to handle weak signals) than others. Your signal might be strong enough to give the full range of channels on one box but not on the other.
As stated, you should try a rescan first. Otherwise see here:
http://www.theanswerbank.co.uk/Technology/Ques tion530614.html
Chris