Not sure what the rep was talking about, but every time I download transactions from Edward Jones, Quicken compares the number of shares in Quicken with information provided by EJ and if different, it offers to create a placeholder. That sounds like a reconciliation to me. It does not compare any loose cash in the account and if you reconcile an investment account, that is the only thing that is reconciled. So by strict interpretation of what the rep stated, I guess Quicken doesn't auto-reconcile, but it only applies to cash, not the quantity of each security.
