It's got to be a grudge. There's no other reason why you would attempt to split up fanbases between so many different consoles. It's ridiculous to announce you will publish two games of the same series on two separate platforms at the same time. What's the logic in that? There's none that I can see, since SE's games have really hit it off on Nintendo handhelds.
Either Square-Enix is seriously considering creating their own console, and want to see the power their IP has for losing consoles, or they have a terrible grudge against Nintendo, and the only way Nintendo will let them publish on the DS is if they create Wii games, the same deal we saw last gen with Final Fantasy: Crystal Chronicles. It's got to be one or the other, because SE is being very reluctant publishing for the by-and-far leader in Japan, the Wii, and they don't truthfully care about American numbers, where the PS3 is in last place, do they?
The facts suggest there's something not being aired in the open here, and history shows the same.