Okay I'm using DeSmuME and the order for Evs is:
Hp
Attack
Defense
Speed
Special Attack
Special Defense
The thing is that the Speed EV is bugged. Instead of elevating the stat it lowers it as well as the Special Attack and Special Defense stat. I have no idea if it's just me or if anyone else is experiencing this. I also don't use any other codes when I use this one.
Edit:
On a side note, the Nature Modifier does not work at all on DeSmuME