We have made some changes to the late fee feature in a new update that should fix the problem you're encountering. *You can download it from: http://www.gophersoftware.com/update
Save the gopher2004.exe file to your desktop and run that instead of Gopher 2003.
Here is something that seems to happen from time to time. A user will set up their late fees to be applied to invoices that are 30 days past due. Then they will have their invoice payment terms to net 30. This will have the effect of not applying the late fees until 60 days after the invoice creation date.
How to resolve this? You could set your payment terms to due upon receipt and then set your late fee to apply afer 30 days. Or you could set your payment terms to 30 days and then your late fee to 1 day etc.