Why there is a discrepancy between the STP submission Report (the YTD gross amount) and the payroll history report

Allowances do not appear on the STP report separately; they are rolled up into the Gross figure. 

There is a specific formula for this; please see the attached spreadsheet which includes their final STP Data as well as a reconciliation using their final payroll summary report. 

The gross value in the STP data and the gross value using the calculation sheet match, so everything reconciles. 

Reason
At the time of STP it includes item separately is uncheck and include in gross taxable amount in STP check.

in Addition Deduction master Setting.

At the time of Payroll history report, the gross amount calculates the (Total Shift value + Allowance Value + Addition value) - (Deduction Value + PayG)

The major field Net Payroll & PayG Amount are matched though.