hey *13 i dont have experience with mu5000 or oo88, but i would try another method ( which i am sure what it does ) to index the axis, and i would compare the result with oo88.
this should be easy if part is simple; otherwise, if part is complex, than there is a way to make it simple
somewhere, something, may have another origin, or shift actual origin, etc
there are different methods for setting operation zero point, and best of them are from code, only after main zero occured
can you share a photo with your part, for the old good days when cameras where invented ? i wont be able to help you with oo88, but i may suggest an alternative
kindly