Dates are very important in Sage 50.  If you run a statement at the end of April and the invoice was paid May1st, it is going to show unpaid.  Could this be your issue? 

If Statements are printed in the same month in which the Customer Payment was applied to the Invoice, then the transaction (Invoice and Payment) will both show on the Statement as they are considered "current transactions" or transactions since the last Statement. After the month in which the Customer Payment has been applied, if you run your Customer Statements as OPEN ITEM, you will no longer see the paid Invoice on the Statement. Please reach out to us for additional assistance, if needed. https://pcosupport.com 

This is not the issue, we do run statements at the end of the month, but invoices that are being referenced as open have been paid earlier in the month.