How do I disable auto-apply when the patient makes a payment?

This is a scenario of what is happening:

Patient comes to appointment.  Payment is taken by receptionist. Provider sees patient and starts an encounter. Billing Department clicks "New Invoice" under "Generate Bills" tab.  Once the invoice is created and approved, it is auto-applying the payment the patient made that day.  Sometimes patients are paying on a balance plus their copay.  So, the entire amount does not need to be added to that visit.  Also, our providers use multiple codes.  If a patient has a deductible and we collect the insurance-allowed amount for all codes that will be billed, it auto-applies all the payment to the first CPT code.  So, the payment is not distributed appropriately. 

This is a screenshot of my settings.  Every time I change "Apply Payments added to the Appointment to Invoice" to "Apply when 'Adjust the available patient credits against the invoice' is selected in invoice" and save the settings, it automatically changes back to "Apply Always".