If you changed your Workers Compensation rate and specified the start date to affect paychecks that have already been processed, your Workers Compensation reports will not match your Workers Comp liability totals. That's because QuickBooks updates the reports but does not update individual paycheck transactions. You need to do that manually.
Go to the Reports menu, choose Employees & Payroll, then click Workers Comp Detail.
Change the date range if necessary, then click Refresh.
Go to the Reports menu, choose Employees & Payroll, then chose Payroll Item Detail.
Click Customize Report in the report button bar.
Click the Display tab, then change the date range of the report if necessary.
Click the Filters tab, then in the Filter list, select Payroll Item.
In the Payroll Item drop-down list, select Workers Compensation.
To see the detail behind any number on a report, click the number when you see the QuickZoom icon.
Compare the two reports to locate differences then adjust the numbers to match, as needed.
Setting up Workers Compensation
Workers Compensation overview