Hello Amy.
Most probably you’ve custom added new income categories and you did not make the new deduction types applicable to those income categories.
For example if you’ve added a custom income type called “My Hourly Pay”, then you need to go to the income categories page, select the income “My Hourly Pay”, and then click Edit. Once the edit dialog comes up, look under “Deductions Applied” and make sure to check the boxes that apply for the SECA and 403b custom deductions you created.
Real Business Solutions Support Team, Makers of W2 Mate and Payroll Mate
708-479-8731