Isolinux is another bootloader that I'm not familiar with.
Your boot sequence now should be:
BIOS --> MBR(GRUB) --> 2ndpartition(ISOLINUX) --> loading kernel, etc
The issue here seems to be in your ISOLINUX bootloader.
I'm really not certain but perhaps you should install Fedora on the USB partition from the Fedora LIVE CD, instead of using the dd command. If you boot from the Live CD I think there must be an option to install it to hard /usb.
*The dd command will also copy the filesystem. The LIVE CD iso file must be ISO9660.
I'll try it with the live cd. I repartitioned my flash so it had 1 partition and used the dd command. I then booted from the usb and it worked perfectly so i know that it's not the iso. I checked the file system and it is a ISO9660 when i used the dd command.