A payroll item may not compute correctly or may not calculate at all on a paycheck for a variety of reasons. 

However, you are at the right place as this article shall apprise you of comprehensive resolving methods to get QuickBooks Payroll is Not Taking Taxes issue rectified in no time.

To find out what is causing the inconsistent behavior in your case, use the following advice. And also check to see if a payroll item for a deduction is set to calculate based on Net or Gross.