Automated pay runs do not lodge for STP as the ATO requires the authority to be "signed" for each pay event, you'll need to log in to QuickBooks Payroll powered by KeyPay and send the pay event. 

The following article covers the process: https://quickbooks.intuit.com/community/Payroll-and-STP/Create-and-lodge-a-pay-event/m-p/275361