@frognfly,
It's not clear how much fits on one scale, but you can get the box in one weighing if you can do the following:
Get 1 of the inner boxes from the first, 2 from the second, and so on. Weigh them at once.
If the total is .1 less than 55 kilos then it was the box you took 1 inner box from, and so on and so forth.
But the scale limitations aren't stated, so if you can't weight that many inner boxes it won't work (note: you don't need innerboxes from them all, you can leave one box out of the weighing and if it weights what it should if they were all 1kg boxes you know it was the one left out).