If you've booted in Ubuntu, you can use dd. In a teminal, type
sudo dd if=input.iso of=/dev/sdX
where input.iso is the source windows iso and /dev/sdX (X will vary) is the destination USB drive you want to wipe entirely and replace with the windows iso. I use gparted to make sure I'm writing to the device I think I'm writing to, as dd will nuke whatever you point it at.