If you want to help solve this please contribute to @mjec's campaign to raise money for representation by a barrister at the AAT appeal http://www.pozible.com/project/183015
I would prefer if the input to the software was published and anyone could verify the outcome. Unfortunately, currently none of this information is published and the whole system is based on trust.
The algorithm is public. It's the Australian Electoral Commission's implementation of it, their software, that's used in public elections that they're calling a trade secret.
The Australian software is not used for recording votes. It's used to assist the counting of physical ballot papers because the Senate vote counting system is extremely complicated. In this environment it's more straightforward to ensure the integrity of the software (as long as it's open and verifiable of course)