To be honest, I can't say as I've heard anyone having this glitch, but then again, I've only used Pokemon Bank sparingly. I'm also not very big into EV/IV training, so even if it were happening to me, I wouldn't have noticed :p
Anyway, as your question is asking about something relating specifically to the games, I'm going to move your thread over to Pokemon Gaming Central, as Pokemon General only deals with the franchise as a whole.
MOVED.