Filing GST Return doesn't include Late Payments

I created a GST return in  app (app.myob.com) for the 6 months ending September. It correctly identified some late payments, which took the refund up to about $3,000.

I then went to File in MYOB (lodge.myob.com) and when I add the GST Return in that system, it does not see the Late Payments and the refund is only about $2,500.

I have had to file it anyway, as the deadline is approaching, but I would like to know why the app sees the Late Payments but not the lodge site?