I reinstalled the same version of Wubi and checked grub.cfg. The lupin entry 
looks like this:
### BEGIN /etc/grub.d/10_lupin ###
menuentry "Ubuntu, Linux 2.6.38-6-generic" {
        insmod part_msdos
        insmod ntfs
        set root='(/dev/sda,msdos3)'
        search --no-floppy --fs-uuid --set=root 8654915254914639
        loopback loop0 /ubuntu/disks/root.disk
        set root=(loop0)
        linux /boot/vmlinuz-2.6.38-6-generic root=UUID=8654915254914639 
loop=/ubuntu/disks/root.disk ro   quiet splash
        initrd /boot/initrd.img-2.6.38-6-generic
}
Apart from changing the target partition it shows that the grub.cfg changed 
after the install - the original entry looks like the traditional wubi entry, 
but then running "sudo update-grub" changes it to this:
### BEGIN /etc/grub.d/10_lupin ###
menuentry "Ubuntu, Linux 2.6.38-6-generic" {
        insmod ext2
        set root='(/dev/loop0)'
        search --no-floppy --fs-uuid --set=root 
b4c80465-f6f6-4e88-a1dc-0321acfe292f
        loopback loop0 /ubuntu/disks/root.disk
        set root=(loop0)
        linux /boot/vmlinuz-2.6.38-6-generic root=UUID=8654915254914639 
loop=/ubuntu/disks/root.disk ro   quiet splash
        initrd /boot/initrd.img-2.6.38-6-generic
}

So I don't think this is a lupin script issue, but rather a grub2 issue.

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https://bugs.launchpad.net/bugs/738345

Title:
  Grub2 entries to boot Wubi incorrect... "Error: file not found, Press
  any key to continue" at boot

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