You have not provided enough information to know what is happening, and no one can see your records. You would need to post screen shots of Edit screens of relevant sales orders and invoices. And have you read the Guide: Monitor sales order status | Manager?
Found the reason some appear invoiced and others not. If I do not include the Order Number on the Invoice or If I change it with the client’s PO number it will not appear as invoiced.
Is there another place I can input the client’s PO number on the invoice?