Ok, finally got down to analyzing this. The problem is that the same county name exists in several regions, which Project-GC doesn't really handle. We then have to suffix the county names.
The fact is that we thought they were. All counties has an extra character after them, which we assumed was a aggrevation of the region, but I now understand that it is not.
We are currently in the process of updating our polygon data for Australia, a region-id will be appended to the names as well, to distinguish them. It may take a few hours for the whole process. Currently building new polygons, after that we will have to recalculate which regions the caches belong to. Then we will purge some cached data that will be obsolete.