To be honest, I can't see why this is happening, however, I'm also not the biggest expert on IV's and co. I know the basic knowledge, and that's about it. My common sense input, would be to ask if you are using action replay, with a code for faster hatching? I've found that some codes that you enter, may have side effects on how they affect the game. (ie: When I played Diamond, all I had was the Pokemon Modifier code that I got from a quiet website. When I encountered a Metapod, it used flamethrower, for absolutely no reason. My two cents, are that, try it without AR, if you are using one. Good Luck!