Among other things, I was told this too. I knew it was wrong then as did my alignment tech. If the flat spot on input shaft is not at 9 o'clock, in my opinion your box is off top center when straight ahead.

How is your toe?

Does your shaft have a straight shot into coupler, or does it hit at the classic odd angle that seems common to these boxes? If so that is likely a clue that all is not right.