Hi Dawn09,
Thanks for your post. If you are already in STP Phase 2 the new ATO reporting categories, like Overtime, Bonuses, Paid leave, are reported separately not included in gross payments. That's one thing to check when reconciling your payroll reports. Make sure the Payroll activity report and Payroll register report match.
The Terminated employees will need their termination date removed and card made active before processing that $0 pay. Once their Summary of payments report is correct you can re-enter the termination date and make the card inactive.
Feel free to write a post if you need further assistance.
Cheers,
Jem