Just to clarify, are you using course import, rather than backup and restore? If so, then this does not result in a full copy of the grade-book. I might be mis-understanding the question.
Importing will only create a grade book columns for any item(s) that are gradable - assignments, quizzes etc. The specific columns that get created by the import process will depend on what activities were ticked, when the import was performed.
It will not bring across any custom grade book columns or gradebook setup.
AFAIK, Moode has always behaved in this way, which makes me suspect that I am missing something in your question.
