My "undeposited funds" account has a balance, but every line item has been deposited, matched to a deposit and reconciled. Why is there a balance and how do I fix it?

You've come to the right place, @jennjo.

I have some information about the undeposited funds' account. This account will become zero balance once you have deposited to the bank all received customer payments on hand. In your case, you'll want to review and manually reconciled this account by following the steps below.

1. Go to Accounting, then select Chart of Accounts.
2. In the Chart of Accounts, find Undeposited Funds then tick the View register link.
3. Tap the Funnel icon on top of the Date column  to filter.
4. Verify each transaction per Reconcile Status. You might want to start with Not recolciled and then No status.
5. Make sure to change the Date. Manually type the letter "R" on the transaction if you need to.
6. Click Apply.

With the above steps, you're able to verify the remaining balance of your undeposited account.

If you need help with other tasks in QBO, you can browse this link here and look for responses that fits your concern.

Let me know if you still have questions or concerns with your account. I'll be there to help. Take care and have a good one.