Did you clear both Academagia catch before you did start the new game? (I personal suspect that the catch also became corrupted during your game with the familiar selection mod)
Also did you run the game with the familiar selection mod with or without the official content also enabled?
If I remember right familiar selection "mod" contain a dated version of the official content and you really ask for trouble if you run 2 ore more official content at the same time. (a real mod is only a few Kilobyte big while a total conversion that contain the official content is some Megabyte big)