Yes, the only way that there will be two different super rates for a single pay run is if a pay category's super rate has been overridden, admin380. I'll discuss this in detail.

The system calculates the superannuation based on the applicable rate for the portion of the pay period that falls within each financial year. Ensure that the superannuation settings are updated to reflect the new rates for accurate calculations.

1. Go to Payroll, then click on Payroll Settings.
2. Select Details. 
3. Tick the checkbox next to Automatically update super rates. Note that this checkbox setting is ticked by default and will only be unticked for a business due to a manual override. If left unticked, QuickBooks won’t apply any super rate updates at all within the payroll account.
   
   
    
4. Once done, click on Save.

To override the Pay Categories super rate please follow these steps:

1. Go back to the Payroll Settings.
2. Choose Pay Rate Templates under the Pay Conditions column.
3. Select the specific Pay Rate Template.
4. Tick the checkbox next to Override, with the Pay Categories that you've chosen (e.g. Salary). And put the exact pay rate for that.
   
   
    
5. When done, select Save.

For more information, kindly visit this article: Superannuation Guarantee changes in QuickBooks Online.

Additionally, you can conveniently pay employee super contributions directly to any registered super fund by utilizing the built-in integration with the Beam super fund clearing house.

We are still here to assist you if you need more help with payroll. We will keep this thread open for your comments.