The passport you show the airline for check in might be different than the passport you would show to immigration. Perhaps better outcome if immigration is the one not confused?
The only time I would see issues is, if one of the passports is for the country of departure and the "other one" for the country of arrival.
Leaving Australia immigration does notice this. And occasionally a third country will notice you seem to have two passports.
Continue with happy wandering?
Fred