I may be wrong but I mentioned it somewhere else here but my theory is that sometime recently. Pretty much since 3.2 as that was the last time I actively played WoW
Anyway, sometime since then I think that maybe they (Blizzard) tweaked the keybindings but only the general ones. For the character ones asking for you to copy the general ones gives me the impression that the character ones are missing something the game needs and thus asks to copy it from general.
It's all theoretical however, but seeing as I the only keybinding issue I ever had was resolved by doing that it makes me wonder.