What you are showing is that Manager believes that somewhere, you credited this customer for having paid enough that either (a) this specific invoice was paid in full or (b) other invoices were overpaid and applied to this invoice or © you received unallocated money from this customer with some of it being automatically allocated to this invoice. (Options b and c are really the same thing.)
To track down what happened, go to
Sales Invoices tab and click on the blue balance due figure for Invoice 1088. It should say 0.00. That will bring up a screen showing all the transactions that have been applied to this sales invoice. You should be able to track down your problem from there.
The reason my first answer may not have seemed on target to you is that you said Manager was overriding your entries and entering the full amount owing. What it is doing is actually telling you the full original amount of the invoice has already been paid.