Thanks for posting your question in the Community, JNR Towing,
I'm here to provide information about how invoice payment works in QuickBooks Online.
If you are using QuickBooks Merchant Services for receiving the invoice payment, it will automatically be posted into your QuickBooks Online account in which all you need to do is to match the downloaded banking transaction to your invoice.
However, if you're not using the QuickBooks Merchant Services, then that's the time that you can manually received invoice payment.
In your case, based on the information you've provided, it looks like you are using the QuickBooks Merchant Services and manually received invoice payment. That is the reason why, it makes the new invoices as paid.
To resolved this, you can delete the payment you've manually received, then match the invoice to the downloaded bank transaction for the payment.
To know more on how to handle this scenario, I'm attaching some helpful articles that you can check: