I have since finished my old game and therefore deleted my old game files and downloaded a new copy, with a wired connection, new save file, zero cheats enabled, and am still having this issue with Kooper sporadically. His coordinates did not line up properly on the path between Hooktail Castle and Petalburg when I tried to use him to retrieve a badge at the top of a pipe during Chapter 1. Came back for it after defeating Hooktail and he was working properly, as well as working properly throughout the whole dungeon.