The relationships between the academies was not set in stone. Even though the Supreme Council's rulings meant that fighting amongst themselves was not allowed, there were still an increasing amount of conflicts in other ways. The conflicts originated from two sources. One was from the fight over benefits in the New World, such as resources or territories. The other was from their history back on Earth.
Even though most of the academies adopted the principles of ignoring Earth politics, it was impossible for there to not be of any influence. For instance, Judge Academy was closer to the European academies, and the European academies were also a tight-knit bunch. Meanwhile, the Russian academy did not have the best relationship with the European academies, let alone America.