Thanks Princess
Doing another payrun for the tax won't fix the issue. All the payroll reports show that it is there but the STP filing for this individual is showing it going in and out and hence not registering at all. If I record again my payroll reports will be incorrect. The issue is that it didn't get picked up on the first payrun for it but it did reverse it when I tried to reverse. If it did the same for the reverse - ie not acknowledge it, I wouldn't have a problem. MYOB reports are correct. STP reporting is incorrect.
The ATO didn't acknowledge the tax amount for the BAS either so as far as the ATO is concerned it doesn't exist.
Is there a way to manually remove the negative amount being picked up in the STP?