Hello there, @tmullins.
I'm here to help share information about running the Profit & Loss Budget vs Actual report in QuickBooks Desktop (QBDT).
Transactions will just reflect on the report if there's a specific class assigned to each transaction or per line account. If the bill created has more than one line account, please ensure to assign a class to each line. It's possible that some of your bill or line account doesn't have a class.
In this case, you must double check the bill you've created that are not appearing on the report.
You see attached screenshots for additional reference.
On the other hand, to learn more about using class tracking in QBDT, you may check this article: How to Use Class Tracking in QuickBooks.
If you have any other questions about running reports in QBDT, don't hesitate to add a comment below. I'll be always here to help you however I can.