Run a repair on QuickBooks to troubleshoot the QuickBooks Payroll Issues. To begin, go to the Start menu and pick the Control Panel. Then click Add or Remove Programs twice. Following that, you must choose the QuickBooks application. After that, select Change or Remove Program from the drop-down menu. Click the Next button in the QuickBooks Installation box now. Select Repair in the QuickBooks Maintenance Window, click Next, and then press the Repair button. Finally, in the QuickBooks Maintenance Complete Window, click Finish.