Thank you for using ezPaycheck payroll software.
I think the most possible reason:
1. Make sure the company period set up is correct.
The tax rate for monthly, weekly and others are different.
2. Please check the number of allowance. - the most possible
The standard Deduction per allowance is: $4,050.00
If this employee claimed number of allowance, it will lower the taxable income.
3. Here is guide about how to calculate federal tax manually
http://www.halfpricesoft...e-Withhold-Manually.aspx If you still have questions, please feel free to contact us.