Summary has two values?

Ok, so I have an invoice thing that calculates the total of the invoice by having a summary field that add up the cost of all the line items on it and displays it in the corner. The problem I have is if I give someone a credit on an invoice it displays correctly in the corner, but in the script that fills out and prints the invoice a value gets assigned to be the summary but it sets the wrong value! I do a credit on a invoice by simply adding a line item with a negative cost, this gets added to the value I have in the corner to show me the total, but on my printed invoices (different layout with different) the total on it is assigned to be the total on my original, but it says too much: The credit does not get added (everything else works). I'm completely stumped, because the total seems to be correct, it's just when I set another field to be the total is gets set to the wrong number.

Yes, I realize I could just make the field on the print layout the grand total and not assign it, but sometimes that field is not set to the total, depending on the invoice. Also no, the alternate value is not getting assigned by mistake, it is just the total without the credit being added. Also the total field is an unstored calculation (the one not on the print layout).