Let me share some insights about how Undeposited Funds account works in QuickBooks Desktop.
Undeposited Funds is used to hold all the invoice payments and sales receipts we want to combine before we create a deposit. When we run a report of the Undeposited Funds account, it will show all the transactions that we're associated with the account.
The sales receipt will not show in the Make Deposits window since these the transaction we're already deposited into the bank account. Also, we can check if the balance of your Undeposited Funds is zero.
Here's how:
Go to the Lists menu.
Choose Chart of Accounts.
Right-click Undeposited Funds, then select QuickReport: Undeposited Funds.