Q: "Can you explain the 'VCE Scores 40+ (%)', what does this actually mean? I have emailed the link you were kind enough to forward to me to a number of parents, all of them have since got back to me very confused.

At the risk of sounding boring I understand the English rating system easily, that is A, B etc.; the school that graduates with 99.8% of it's students achieving A and B scores is rated higher than the school that achieves 99.0%."

A: It's the abbreviation of "Percent of study scores of 40 and over". This is about subject scores. A perfect subject score is 50. "Percent of study scores of 40 and over" (rather than ENTER score) is the official index for school's performance. The scoring system is very complicated. Even the parents here can get confused. That why we need score calculators:
VCE ENTER score calculator
HSC UAI calculator

BTW, ACER (Australian Council for Educational Research) chief Geoff Masters has called for an overhaul of the letter-based rankings A-E in schools.

Related:
What is Median VCE study score?
Does "Percent of study scores of 40+" mean ENTER 80% in the state?