Thanks for providing us the in-depth details of your payroll issue, chrisc1.

I appreciate you for checking out the setup of the Bonus payroll item. Yes, you're right, if the employee has a $1000 bonus amount on their paycheck, the amount in the Company Summary for Bonus should be $30. Cases like this, we can run a Payroll Item Detail report. Then, check if there are prior paychecks that did not withhold the bonus amount in the Company Summary section.

Here's how:

1. Click Reports on the top menu.
2. Choose Employees & Payroll.
3. Hit Payroll Item Detail.
4. Manually enter the date for this current quarter in the Dates field.
5. Look for the Bonus company deduction and review if there are zero figure in the Amount column.

If there's a discrepancy in the amount for the last paycheck, we can manually adjust it. This way, the correct 3% of the bonus amount will be reflected in the Company Summary section. 

Here's how:

1. Click Employees on the top menu.
2. Choose Payroll Taxes and Liabilities.
3. Tick Adjust Payroll Liabilities.
4. Adjust the date period in the Date field.
5. Hit Company in the Adjustment for: section.
6. Select the bonus item in the Item Name column.
7. Enter the discrepancy amount in the Amount column.
8. Type the details in the Memo column on what the adjustment for.
9. Tap OK.

To learn more about adjusting payroll liabilities and payroll items calculating incorrectly on the paycheck, please refer to these articles:

• Adjust payroll liabilities in QuickBooks Desktop
• Payroll items on paycheck are not calculating or are calculating incorrectly

Keep me posted if you need a hand with running payroll transactions and reports or any QuickBooks related. I'm always here to help.