The Pay History in an employee's card is stored on a monthly basis, and you can select the Month, Quarter or Year to Date values to report on:
To identify where the discrepancy lies, you need to start with a wide date range then gradually narrow this down to pinpoint the cause.
Start by comparing the Year to Date values in the card's Pay History with the figures in your reports for the full payroll year (select Year to Date in the Show Pay History for field). If the values differ for the year, re-run your reports for the 1st quarter and compare the values to the Pay History for 1st Quarter.
When you identify which quarter has the invalid information, re-run the reports and compare the Pay History month by month.
The most common cause of reports not balancing is that the pays are being compared against the Pay History and due to the dates in use, more or less than a whole month is being reported and compared.