You do not say if you are using Qlikview or Sense. This should probably be moved to a more appropriate space (not related to Qlik DataMarket).
I assume you are suppressing nulls in one or more dimensions. If the expressions for the null lines have values,you will be suppressing those values as well. Are the total modes using expression totals or sum of rows? If its the latter, then the total will be reduced, otherwise it will depend on your data structure and expression.
I suggest that you upload a small sample qvw or qvf that illsutrates the problem.