Create a one time charge that matches the origianal charge amount and due date.
Select the payment under payment history that created the zero balance due charge.
When in the edit page. Move the payment amount out of the origianal charge and into the one time charge you created.
Now delete the original charge that was showing in the income form with zero due.
If you have two charges such as rent and late fee. The late fee may be the charge that created the zero balance issue. Make sure when entering the payment to apply the payment (next to amount due) to rent first and late fee second.
This way the late fee is the charge you are going to create a copy of as a one time charge and delete the original.