I think you're expecting results way too fast. It's not as if you beat 2 Ferroseeds holding the Macho Brace and your defence will suddenly go up by 1. You need to do a lot of training before any EV gain is obvious, and even then it'd only be obvious at Level 100.
Also, your Cresselia might have EVs in other stats already, and might have "used up" all of her EVs. That's also a possible reason as to why she's not gaining EVs properly. If you didn't battle her at all and didn't get her from a trade, then it's because of the first reason that you're not seeing any/ much stat gains.
If you want to check your EVs, you can always call Bianca. She will give you some indication as to where the EVs on your Pokemon are.