Hi there,
Most probably you are not using one of the built-in income types to pay your employee. In this case you will need to go back to your company, edit the custom added income (that you use to pay this employee) and make sure the tax levy deduction is checked under the list of deductions for that income.
Real Business Solutions Support Team, Makers of W2 Mate and Payroll Mate
http://www.realtaxtools.com/
support@realtaxtools.com
708-479-8731