are we eligible for 144hr Visa free transit twice?

You are definitely eligible for 144 hour visa free transit in both Shanghai and Beijing. This is, of course, valid in case if you have mentioned your all stops. I'm telling this for purpose because there are no direct flights between Beijing and Brisbane. So, you should take care about this detail because within 144 hour visa free transit, you are not allowed to have two consecutive stops within mainland China. Please, check your itinerary carefully and see if there are some problematic details.