Hi WMack
From what you've described it sounds like the casual YTD amounts have been removed from the employee card>>Pay History. Run the Payroll activity and Payroll register reports, if they're not the same then that is what is causing your issue.
You'll need to restore a back up and change the employee card>>Pay History to include the casual YTD amounts. Then process a $0 pay with payment date as 30 June to update STP.
Please let me know how you go.
If my response has answered your enquiry please click "Accept as Solution" to assist other users find this information.