Our software calculates the Federal Withholding based on these factors:
Number of allowances/dependents
And, these are the possible reasons why it's not calculating the tax:
Annualized salary exceeds the salary limit
The gross wage of the employees are too low
Thanks for confirming that the employee's profile is set up correctly. Let's try to manually calculate the employee's paycheck, then check if it matches with QuickBooks. To help us figure out the exact withholding amount, go through the IRS 2018 Publication 15. Use the Percentage method (page 44-45). This is the same method used by QuickBooks to calculate the Federal Withholding.
Get back to me if you need more help. I'll help you in any way I can.