Bonus Payment not Showing in Gross Payments on YTD

I know there are already a few discussions around this, however, I'm unsure that they address this specific query.

I have one employee who left towards the end of last year, their gross YTD payment figure on the EOFY finalisation screen does not reflect the bonus payment that was made to them when they left, whereas, for all other employees their bonus payments are included in the YTD gross payment figure on the EOFY finalisation screen.  I have checked the summary of payments report for the employee who left, against a report for a current employee, and in both instances, their bonuses are 'coded' as bonuses in that report, so why would one be reflected in the YTD gross payments. and not the other? 

We also paid the employee who left a lump sum payment for their unused leave, and I understand from other questions that they aren't reported in the gross payment figure, but I'm confused as to the discrepancy between how the bonus reporting has arisen. 

Also, if I finalise this employee's pay, is the whole amount we paid them reported to the ATO, or only the gross payment figure?

Thanks 

EDIT: I have resolved this issue for the employee in question by removing their resignation, however, I have an issue with two former employees who were paid bonuses only in the financial year.  I didn't resign them as I knew we would need to pay them the bonuses after their leaving dates, however their payments are not showing in the YTD total figure, and I cannot make head nor tail of how the full summary report has been calculated, it does not add up to the activity summary total, and I can't make the taxable payments figure line up either.