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.