Thank you.  I followed those steps to verify the deposit is linked to the invoice, but it seems I'm still missing something.

When I double click the invoice, the payment status shows as paid, and below it indicates "1 payment made ($100)".  When I click on the "1 payment made" link, it takes me to a "receive payment" screen.  In the Outstanding Transactions field, the correct invoice is checked. 

Scrolling down to the Credits section, nothing is checked.  I can see that the $100 deposit is there (though unchecked), but in the Original Payment column it shows $80, and next in the Open Balance column it shows $20 (numbers fictionalized for ease of understanding).

What does any of this mean?