I think the bottom line is that you may be seen as an 'overstayer'. You entered under one passport and there may not be a record of you leaving.

What problems will that cause? Who knows. You may (or may not) be able to get a new electronic travel authority in the future. You may make it to Australia and be stopped for questioning (I'd keep your outbound boarding passes to the USA from this time, and any record you have taken the flight (such as FF miles posting)).

Or nothing may happen.

Sounds like trying to sort it out is proving difficult. Unless you might have an urgent need to travel to Australia in future - one where you absolutely can't wait if your ETA request is refused - I would probably just let it go and sort it out later.