Did you start a new game with the Hardcore mod installed (or similar) and then swap after making a save file? The Buster Sword in the Hardcore mod is unique in that it now has Vincent's Death Penalty effect (more kills = more damage). Thing is, to set it's initial power to what it is usually for the start of the game (40-50 damage) Gjoerulv set Cloud to have something like 1000 or so kills when starting the game, with the limit kills required adjusted to compensate. That means loading up most other mods with that save file will have Cloud instantly learn all three levels once he finishes a fight.
That's exactly what I did so that explains it. Thanks a lot for the answer Sega Chief!