Hi BAMGreg
Thanks for your post. If payment transactions are not appearing in the Prepare Bank Deposit window go to Setup>>Linked accounts>>Accounts & Banking Accounts and check the account selected for Bank Account for Undeposited Funds. Typically this would be the undeposited funds account.
Then go to Transaction Journal>>Receipts tab>>locate one of the payment transactions>>click on the zoom arrow to open the transaction and check the Deposit to account is the same account as selected in Linked accounts.
If it is the same account, in the Prepare Bank Deposit window make sure the filters are correct. Also check that the bank deposit transaction hasn't already been recorded.
If the account is different you will need to change the Deposit to account in the payment transaction to the account selected in Linked accounts.
If you continue to have trouble with this please send me screenshots of a payment transaction, the Linked accounts window and the Prepare Bank Deposit window. Make sure sensitive information is removed from screenshots prior to posting on the public Forum.
Please let me know how you go.
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