The Upside down flag is usually imported for indicating when a country or entity is in distress. This was not the case on the flags that were presented by the during their battles in canberra. When some of the leadership were on alta-vista to research their plan of action, they discovered that the rest of the world thinks that Australia is upside-down.
So as to ensure that the Eleventeen billion people watching across the world were not confused as to who was protesting, they opted to invert some of the flags.
The Non-upside down
So as not to confuse their own protestors as to believing they were on the wrong side of the planet, the leadership made sure that some of them were the correct way around.
The Eureka Flag
A lot of the leadership in these protests that are viewed around the world opt for the Eureka flag, this is because there is no up-side or down-side so no one can get confused.