Check configuration for WHMCS as there is something not working correctly

I am having this problem where WHMCS is generating new invoices, some of which have already been assigned to other clients, after the payments have been made. eg, invoice 22984 was paid 2/10/13 with the due date being 1/10/13. The client was then invoice today (15/10/13) an overdue notice for 22942 which belongs to another client and was overdue. What in fact happened was the later invoice number 22942 was used to replicate the original invoiced items but could not be paid from the original client as it belonged to another client who has not paid. His invoiced items where different but for the same dollar amount. How do I fix this as many clients got overdue invoices for payments they have already made and those invoices are attached to other clients. I need someone who has experience working with WHMCS and knows what the configuration should be. Also will need to troubleshoot the problem at hand.