> so why the plane behaved like it did with it's back up system assumed to be working?]
If I've read the article right, they noticed one of the airspeed sensors was wonky but the backup was fine, so continued the takeoff. After takeoff something else went wrong and the flaps came up but not the slats, which triggered the return to Brisbane. Makes sense, the slats are only for low-speed flight.
I was expecting a giant wasps nest behind the slats to be the problem, but it sounds like something was reliant on the wasp-infested airspeed sensor and gave up the ghost. There's probably a safety system that stops the slats retracting if the computer thinks you're going too slow.
The Air France incident (if it's the one I'm thinking of) was a frozen attitude sensor. They were trying to test the anti-stall and had deliberately stalled it, but the computer didn't know and did nothing about it.