I am sorry to report I seem to have experienced the same behavior as Rissoux. So far I have only played two games (I only discovered this mod a couple days ago) both on the same map; the first went without issue, but on the second game, when issuing a 'move' command to a different gravity well, sometimes ships would wander outside of their gravity well without entering hyperspace. It seemed to me like scoutships were particularly affected (both mine and the AI's). The only fix I found was to order the fleet to the edge of the gravity well, and then order them to jump.
On a more positive note, I would like to say how impressed I was with the quality of this mod. It is obvious that a lot of time and effort went into making it.