Run a repair on QuickBooks to resolve the quickbooks payroll issues. Starting from the Start menu, choose the Control Panel. then click Add or Remove Programs twice. Selecting the QuickBooks application is the following step. From the drop-down menu that follows, select Change or Remove Program. Click the Next button as soon as you see it in the QuickBooks Installation box. Select Repair in the QuickBooks Maintenance Window, proceed to the following step and then click Repair. In the QuickBooks Maintenance Complete Window, click Finish to finish.