Hi Tania, 

Thank you for getting back to us on this. 

Based on what you mentioned, it is a bit hard to determine why it happens. 

I would suggest contacting our support team so we can take a better look with you in the payroll setting over a screen-share session. Please found the contact details of our support team in the link below:

https://help.quickbooks.intuit.com/en_AU/contact

Thank you and please let us know if you require any additional assistance.