QB Issue Resolution:

Where did you add the Bonus item?

How 401k calculates depends on the sequence. It calculates the payroll item above it. When you add a payroll item under Earnings and Other Payroll Items it is 1st in the sequence, and the 401k calculates from those items.

I have attached screenshots for your reference.

Resolution for Issue 'Where do you find how 401k calcs on different PR line items like bonuses? I have a line item that calcs different on 2 employees.' available: Yes (Solved).
Source: Intuit Community forum.

Where do you find how 401k calcs on different PR line items like bonuses? I have a line item that calcs different on 2 employees.: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

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