When you create the invoice it will debit the debtors and credit to what ever income you use.When you receive the payment the debtors account is credited and the account you use to receive the payment is debited.
When you create/select receive payment are you selecting the correct debtor/customer, are you viewing the debtors account and able to see the invoice being debited and the corresponding payment being credited?
Debtors is a default account that QuickBooks uses to track customer transactions and is standard in double-entry bookkeeping systems.
When you enter an open transaction, i.e. invoice, it will automatically post the total amount to the debtors account as a debit. When you record the payment on the invoice this will post the payment as a credit to the debtors account. An easy way to view this in action is to open the invoice and payment and go to More > Transaction journal to view how this posts.
When you view the invoice transaction journal this should show two lines - one posting to the sales account and one to the debtors (if you are using VAT there will be an additional line to VAT control).
Please let us know if this does not clarify your query,
You can open the invoice on a browser by going to Sales > All Sales > Locate invoice in list > Click into invoice to open.
A grey toolbar will appear on the bottom of the screen with the option for More > Transaction journal.
You can then view the payment by opening the invoice, selecting '1 payment made' > click the date to open payment, and go to More > Transaction journal.
I was having a similar issue and it was down to user error.
The report you are looking at is a transaction report and shows all invoices and payments/receipts so it will look like the invoice is still outstanding, but the payment/receipt is lower down.
You need to be running:
Accounts payables ageing report (what you owe out)
Accounts receivables ageing report (what people owe you)
Hope this helps!