I'm having a similar problem.  I pay contractors via direct deposit and when I schedule a contractor payment, the ledger shows the pending withdrawal but it also shows a pending deposit for the same amount.  It does the same thing whenever I enter an expense into the ledger manually: it automatically creates a deposit entry for the same amount.   When I delete the deposit line item, the expense line item is also deleted.  The screen shot is an example.  I scheduled a contractor payment for tomorrow, but the ledger entry shows an expense and a deposit for the same amount.  Why is quickbooks generating a deposit line item when I schedule payments?  This is not a case where it's downloading entries from my bank.  It's generating the deposit line item before I've even made the payment.  See screen shot. Please advise.