Hi there, cjbarber1. Thanks for joining the thread.

In QuickBooks Online (QBO), there is a feature that offers automation. It might be, turned on, that is why it marks your invoices as paid. 

Here's how to check:

1. Click the Gear icon at the top.
2. Select Account and Settings.
3. In the left menu, tap Advanced.
4. Hit the Pencil icon in the Automation section.
5. Check if there is a check-mark in the box next to Automatically apply credits.

If yes, then, that is the reason. To turn off, remove the check-mark in the box next to Automatically apply credits. Then, tap Save and Done. 

After that, let's open the created invoice that was marked as paid and delete the applied payment. This way, it'll mark the invoice as unpaid.

1. In the left menu, click Sales.
2. Locate the newly-created invoice.
3. Select on the 1 payment link at the upper right hand above the PAID payment status.
4. Click the date link.
5. On the Receive Payment page, select the invoice.
6. Click More at the bottom.
7. Choose Delete, then choose Yes to confirm.

To learn more about receiving payments and applying credits in QBO, see the below articles:

• Record invoice payments in QuickBooks Online
• Handle a customer credit or overpayment in QuickBooks Online

For future reference, you might find this resource helpful: Record a customer refund in QuickBooks Online. 

Please let me know how it works. I'm always here to help. Have a great day!