You could try to repartition it, using fdisk:

(unmount the USB stick first)
sudo fdisk /dev/sdX

- create a new partition table (not sure which command, enter "m" for help)- I think it is "o"
 - create new partition : n
 - select type "primary" : p
 - select number 1 : 1
 - select default begin: just press enter
 - select deafult end: just press enter
 - write new partition table and exit: w

(just in case unplug and replug the USB stick, so the kernel uses the new partition layout)

Then format the partition: sudo mkdosfs /dev/sdX1

Then you can follow the instruction from http://www.pendrivelinux.com/install-grub2-on-usb-from-ubuntu-linux/
from the point 5 on.

Hope this helps.

MfG,
David

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