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The Simple IRA item is supposed to be calculated after a Prem 125 item is deducted from the gross pay. As per IRS (https://www.irs.gov/retirement-plans/simple-ira-plan-faqs-compensation), "Compensation doesn’t include amounts deferred under a section 125 cafeteria plan".
In Quickbooks, when a Simple IRA item is set up to calculate on a percentage, it calculates directly from the gross pay even if there's a Prem 125 item.
You'll want to reach out to our Payroll Specialist so they can further check your payroll setup. The new "Help" menu interface:
For the old "Help" menu:
Also, you'll want to check this article about supported pay types and deductions: Supported pay types and deductions explained.
Post again here if you have more questions. I'll be here!