Put the usb hard disk in the last position of grub device names for hard disks.
Usbshift is a command that it is run automatically at the boot of Super Grub Disk. Its behaviour is the following one: If Super Grub Disk is being run from (hd0) device (usually when you run it from a usb) then a shift of all the drives is done. This way the second hard disk becomes the first hard disk (what it is usually). And the pendrive device (the device with SGD in it) becomes the last grub device.
If Usbshift does not detect that SGD is being run from (hd0) it does nothing.
You are not supposed to run usbshift yourself but you should know about it because if you are used to create your own menu.lst for usb you will probably think that (hd0) means usb while in SGD it only means first hard disk.