Hello eoldman@yourbott,
Welcome to Community! QuickBooks Online provides the ability to create and auto-apply bank rules, so your transactions are matched effortlessly. I can understand how your work is impacted, when the transactions aren't being recognized, based on the rule you've created. I would be happy to provide some insight here!
When the Automatically confirm transactions this rule applies to, has the toggled set to on, transactions with the eligible criteria should be automatically applied. When this fails, the rule may contain multiple conditions, and is set to ALL instead of ANY. If you need the transactions to comply with both conditions to be added, it should be set to All. If you want it to be based on just one of the criteria needed to be added, choose Any. In addition, the rule may have the Include the following option set to Is Exactly rather than Contains.
If the Auto-add option is toggled to On, and all areas of the rule are properly set, but isn't working as designed, I recommend reaching out to our Customer Care team outside of the Community. They'll be able to view the issue in more depth, and gather the necessary information to escalate it for further investigation with our Development Team.
Feel free to reach back out with other questions. We would be glad to help!