Try each of the following steps in order until the issue is resolved:

1. Check the date ranges and Constituents being included on the general tab of the report and criteria tab of the query.
2. Check the filters to make sure they are the same.
3. For gift types, uncheck exclude zero amounts and pull over all gift types or match the gift types to be the same as they are in the query.

For further troubleshooting steps, see Reports do not match in Raiser's Edge 7 (BB76601)