I recommend reaching out to our Payroll Support for further assistance. Rest assured, they have the tools that can look into your account and see why your Federal Income Taxes aren't being calculated when you run Payroll. They can get into a screen-share with you to see if your Employees and Company Information is properly set up to get the correct calculations when you do Payroll. You can let me know how the conversation goes by leaving me a Reply.
I'll be here if you have any additional questions or concerns. Have a great day!
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