It could be that the School Years have not been correctly applied to the Discount Rate Rule. To verify, go to:

• Fees, Billing & Payments
  
• Setup Fees, Billing & Payments (top right) 
  
• Discount Rates
  
• Click 'View Discount Rules'
  
• Edit the Discount Rule and ensure School Year(s) are selected
  
• Save to apply.