By default, when you check in an item for a patron in the Check In tab in Circulation Desk mode, Millennium clears the Total box of fines the previous patron accumulated. That is, the amount is set back to zero as soon as a new patron checks something in, even if you don't Close the current record.
If this option is selected, Millennium continues to display the fines accumulated by previous patrons. This allows you to collect fines for multiple patrons, e.g. for a family.
To clear the Total box before you scan an item, click on the Close button.