Hello Keith,
May I add another check, which unlike Andrew's doesn't need you to cut anything.
Taking your pictures as a guide with the clock moved from front to back of the box and the recorded difference of 0.17mm, what happens if you do the same test on the other side of the box without moving anything except the mounting of the clock?
Assuming the box is square, as it should be, then I would expectthose readings will be reversed. that will reassure you that the box at least is as you believe.
You don't I think say how you aligned the box in the first place, was it by try square across the table? Again, testing on the other side of the box with that, using the inside edge this time should give the same degree of fit. Now turn the square over and butt it up and repeat the steps above. If the try square is wrong that will show as a gap on both sides.
These are simple tests and cost nothing to do except a little more time. They may help you sort out which things are wrong. I think the box would be true from it's stated quality, the mill also to be right and the try square wrong in that order of probablity. Even testing with another try square might reveal something before you condemn the mill and it might save face if challenged as you are likely to be.
I hope that shed some light
Brian