Can't tell you where you went wrong, but I can confirm that Administrator III is working properly.  I currently have 4 units with the trait, and as expected, have -40 global unrest from them.

I can also confirm that it is working in version .80

careful about modding the core files. I presently have everything backed up and when I play the game, it is actually unmodded version of the game (I rarely play a modded version, oddly). The only mods I have in my game are actually future fixes to the game itself (which I've tested and confirmed is an actual fix).

I've had a similar experience with a level 1 custom champion. 

At level 1 the Administrator skill doesn't show up in the champion's portrait screen.

At level 2, once Path of the Commander is chosen, the skill does show up in the skill tree but still doesn't appear in the portrait screen. Considering this as a disqualifying turn of events, I didn't test further to see if the skill actually gives the intended benefits.

As I haven't seen this happen with other paths' base skills (such as Precision or Spell Resistance), I think it's a bug specific to the Administrator skill.