Do the red levers move when the box is off the bike?
If YES, have a look at what moves underneath the box and make sure you align everything before trying to lock the box onto the cradle.
If NO and the red levers do not move with the box off the bike, then as above, the mechanism must be snagging on something.
Maybe even take the barrel out so it's all unlocked and try the the red levers first and then mount, before fitting the locking barrel?
I also had a nightmare on mine, the barrel would work without being fitted but when in the cyliner, I could put the key in but when locked I couldn't remove the key. Took it to the dealer in the end, who advised that the last wafer should not be used.
HTH