Cafe, if as you say the box went through the 'normal' check in, then it would be very possible that it didn't have the requisite form/disclaimer filled (since they go as 'cargo' effectively) and they can't take it. So, a bit of the fault of the handling agent BUT the airline was doing the safe thing.
I've received many an item being taken as either accompanied luggage or as 'cargo' packed in a box. Many times the box was not adequate to secure the item concerned OR the descriptions given were vague therefore we needed to call the passenger back once they had checked in to determine a) the contents and b) if there were any dangerous goods. Some people have n idea they can't take certain things.
For example, "car parts" turned out to be a small petrol engine, still with small amount of petrol in the tank!
Of all the boxes of freight I ever processed, probably 60% did not contain what the dclaration said or had vague descriptions that needed to be re-written. So yes, a box 'can' be more threatening than a suitcase (purely because people seem to put things in a box they would never put in their own bags- bleach, fireworks, dynamite (!) etc...)