I cannot say much to that.
We have such copied system too, but if I create the data myself there, then I usually do not find the error that a user has in production, I can just tell the user that the design works, so it is not directly comparable for me. Hence it would be interesting to know what happens if the user does ME56 in production, only this could really show if there is some data missing.
I think you should take this small effort to implement this Z-report to check for the root cause, this is certainly cheaper than wasting a few more days of your time by guessing and trying.