Payment not getting applied - when using Apply payments by Invoice

Hi,

When we are trying to make a payment by invoice, the payment is not getting applied to the charges. It is shown as un applied amount.

What we did:

1. Enabled Apply payments by invoice

2. Created a target key and enabled payments by invoice

3. Enrolled student into the class

4. Calculated Tuition for the student - which included Term fee and Course fee

5. Posted partial payment thru cashiering on the student account

6. Generated Invoice. Here on the invoice, it shows both charge and payment on Invoice and shows net of charge as the balance

7. On verifying the student account, the payment is un applied