I've had really bad luck using syslinux to boot from usb drives. Grub was much more reliable, although more difficult to setup.
grub-install --recheck /dev/sd? --root-directory=/boot/place_for_files
you will then need to point grub to the kernel and initrd using the grub.conf file in the /boot/folder. I copied the contents of my /boot folder from fedora into the /boot folder on the usb key. after tuning up the grub.conf file it worked. You may need to play around with the root (hd0,0) or root (hd1,0) to get the key to work, as it seems like the bios changed the drive orders based on whether the key is plugged in as boot time. Anyway - it was way more reliable than syslinux.
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