Good to see you here in the Community, @Wolverine2. 

You've got me here today to share some information about the matching transactions in QuickBooks Online. 

If you categorize the bank transaction to Accounts Receivable, the customer's balance will be negative or there is a credit available. Once the customer pays the invoice, you must link the available credit to the invoice and zero the total amount to close the invoice. 

To answer your first question "Could that be the reason why they are still showing as A/R?", no. It will still show as Accounts Receivable because in that reporting period there's an A/R transaction regardless if paid or not. 

You can change the Accounting method in the report to a Cash basis. For your reference, you can also check out this article for more information: Change the accounting method.

Make sure to check the reporting period is correct. You can also add the Debit and Credit columns to have an idea about the Profit & Loss movement. 

For your second question "How do you correct the problem without going back and Matching?", if you still getting incorrect data after changing the Report period and Accounting method, you need to UNDO the added bank transactions. After that, you can Find a Match to the invoice. 

Once you split the bank transaction and you did not affect A/R, it will cause a duplicate in your register. To fix this, you need to UNDO the bank transaction again. 

Here's more information about adding and matching transactions in QuickBooks Online: Download, match, and categorize your bank transactions in QuickBooks Online.

If you require more information about matching spit payments and Profit and Loss reports in QuickBooks Online, please let me know. I'm here to help.