First of all a philosphical point. The Canonical Millenium's End Campaign appears to assume a world where corporations are running amuck. My own campaign assumes a world where both corporations and governments are running amuck, which IMHO is worse. Some might think that the combination is impossible, but I (obviously) do not.
The first explanation is that levels of power vary strongly with the place, the situation, the time, the people involved, and the area. In some places different powers (givernments, corporations and other organizations) work together or towards the same goals, leading to massively invasive exercises of power. In other places they balance each other out, leading to total anarchy.
The second explanation is that groups who feel their power slipping away from them in some areas tend to overcompensate in others. The reasons might be deception, frustration, self-deception or a mixture of all three, but the actions still take place. A typical example of this can be found in the Miami Sourcebook: contrast the powerlessness of the police in the 'Red Zone' with the abuse of official powers of the 'Undercover Blues'.

The philosphical basis of my Millenium's End campaign can be summed up in two sentences:

All organizations become evil (ie ruthlessly self-serving), unless individuals keep them good.

Hidden organizations, ie conspiracies, factions, schisms etc, are virtually impossible to keep good.