credit can not be applied to pay bills

I have multiple old bills for the different suppliers. All have credits available that can be applied to them. When I go to Pay Bills, it asks if I want to apply the credit. I select the appropriate credit, and choose pay bill. For some reason the credit never applies. So the bills are staying in the system as incomplete since years ago. How can I fix this please? Meanwhile, when I go to supplier centre to see whether the outstanding amount matching with "pay bills amount", the balance are showing zero. I assume our external accountant had done the journal to clear all old outstanding amount but not clear in "pay bills"?