Yes, the mass imbalance in the Rate / Period panels is the way to assess the imbalance in the mass budget. In contrast, the fluid imbalance in the Rate / Period panels is the way to assess the imbalance in the fluid budget.
Perhaps the following discussion may help you to reduce the imbalance: http://forum.mikepoweredbydhi.com/index.php?topic=2263.msg5246#msg5246