Box 13 on form W2 is not populated based on information set up on the W2 form in Payroll, Tools, Modify Forms, W2 forms.
The boxes are populated based on information on the setup of the Employee at the point in time the form is being processed.
In Payroll select Setup, Employees. Select the employee that needs to have a box checked or unchecked in box 13 on form W2.
Click on the Misc Info Tab.
Check or uncheck the Retirement plan and/or 3rd party sick check boxes as needed.