We'll have to check the setup and status of these payments to know why they're not showing in the Batch Deposit section, watravis2.
During the setup process for Payments, you'll be given three options to post the online payments. You can either choose from:
A bank account
Different account in your Chart of Accounts.
You can go back and review your Payments settings to see what option was selected. This is to know why you're not seeing the online payments in the Undeposited funds account.
I'd also suggest checking the status of these payments. If they're still pending, they won't show in the Batch Deposit screen. It will take another two business days to be posted after it has cleared the customer's account.
Please let me know if you have more questions on this.