I paid an employee with a check, then ran payroll and discovered I was off by 9 cents. original check cleared and reconciled but new payroll transaction is not reconcilin

For 9 cents, make an adjustment to bank service charges or office supplies.  9 cents is immaterial and not worth you time trying to fix it especially since tax returns and financial reports are usually cents-less.

Hello there, @manager-store001.

Thanks for posting your concern here in the Community. Let's verify and ensure that the information in Quickbooks Online (QBO) matches with your statement. Then, let's make necessary changes to it so you can reconcile your transactions successfully, Here's how: 

1. Go to the Reconcile page, then, select Edit info.
2. Double-check and verify that the Ending balance and Ending date information matches with your statement in the Edit the information section.
3. Edit the Ending balance and Ending date if needed.
4. Select Save.

You can also check the total number of transactions in Quickbooks and compare it with that of your statement. If there are too many transactions from your QBO, these may be signified: 

• Transactions were mistakenly marked as cleared.
• Transactions were entered twice in QuickBooks Online.
• Deposits or charges that were entered as payments or payments entered as deposits or charges.
• Bank charges were entered and selected twice. 

If this is the case, see the article: Fix issues when you're reconciling accounts in QuickBooks Online. It helps you learn about how to find and fix reconciliation issues. 

I also recommend working with your accountant for proper guidance in locating the error in case you still can't get the difference to $0.00. 

I'd be happy to know how it goes, @manager-store001. We're always delighted to help. 

I think KathrynjoyceO is over thinking the situation.  You wrote and manual check, then you entered it in the payroll module and the check was off 9cents by the check you wrote.  Go with the number that the payroll calculated.  Adjust your bank statement up or down by 9 cents to make it balance and code that 9 cents to a bank charge.