Hi CSullivan
Thank you for your post. I'd like to extend you a warm welcome to the Community Forum, I hope you find it a valuable resource.
In this regard, if your employees receive the correct payment summary but additionally indicate two additional incomes, you can just disregard them. Or Is it showing two payment summaries once you finalized on ATO? You can also check if the payroll reports match. Can you please send me a screenshot of the first two payments so that I can look into it?
I happy to assist you.
Thanks,
Cel