Hi jdillon
The Payroll activity report gets it's data from the pays recorded in Process Payroll.
The Payroll register report and STP YTD verification report/Summary of payments report get their data from the employee card>>Pay History.
When the Payroll activity report and STP reports don't reconcile the first troubleshooting step is to run the Payroll activity and Payroll register reports. They should always be exactly the same. If they are different it means that a manual change has been made to the employee card>>Pay History. Any payroll changes must be recorded through Process Payroll so that all payroll/STP reporting is correct.
If the Payroll register report is incorrect you will need to restore a back up taken prior to 30 June, change the Pay history back to what it should be, process a $0 pay with payment date as 30 June to update STP. Wait until that report is accepted before rechecking the YTD verification report.
The Pay History is in the Payroll Details tab>>Pay History on the left side tab bar.
Please let me know if you need further help.