Under the Alternatives heading there is a field that refers to when the inventory took place. Today's date is entered by default, but can be changed to the date of your choice. For example, you can enter a past date, so that the registration of the same part from different lists will take place on different dates, but when the inventory date is the same date, the total balances are added and the difference, if any, will be correct.
If a previous physical inventory has been performed on the part on the same date, a question will appear (when you have entered the quantity and tabbed to a new row) asking whether the balance should be added to the previous inventory (this is selected by default). If you click No in this window, the report will instead be seen as a new physical inventory and the inventory difference is then calculated against the current balance at the time of the reporting.