Comment 2 for bug 566490

Agostino Russo:"If there is any extra logic to find out the "right" partition into which install wubildr, without spamming the HD, I will be glad to add that in."

How about choosing the one with the boot flag set? That should solve this.

Although, the lupin version of grub-install will need to be aware of this too - right now it doesn't recognize wubi unless the wubildr is on the same partition as the root.disk (https://bugs.launchpad.net/ubuntu/+source/lupin/+bug/604417)