Under the Sales Invoice tab, choose any invoice and, under the “Balance due” column click on the blue number. (For an invoice Manager believes is paid in full, that number should be zero.) You should see a list of at least two transactions. One should be described as “Sales Invoice” and should list the invoice number. The amount should show in black. The other (if the invoice was paid via a single transaction) should be the offsetting payment in red, a negative number. It would typically be described as “Receive Money.” If the invoice was paid in more than one installment, there should be more than one such entry.
The payment amount (or sum of amounts if paid in more than one transaction) should exactly offset the invoice amount. Otherwise, Manager would not be telling you the invoice is paid in full.
You don’t need to share any details about your clients or pricing. But please describe what you see when you perform this procedure. If you don’t see see something similar to what I’ve described, your problem does not lie with Sales Invoices, but with something else you are doing.