Ah... this is because sometimes Linux will see your USB flash drive as the
first drive. And guess what, by default image jobs will always assume you'll be wanting to deploy to that first disk.
A way to resolve this for Linux Automation is to ensure the disk drivers are loaded before the usb drivers. This can be done by unloading the lot, and then loading the drivers back in, in the correct order. This can be achieved by placing the following little script into your startup folder using bootdisk creator. Call it disk_modules.sh,
#!/bin/bash
# Unload disk and usb storage modules
echo 'Unloading disk modules...'
rmmod ata_piix 2>/dev/nul
rmmod ahci 2>/dev/nul
rmmod usb_storage 2>/dev/nul
# Now reload the modules, disks first.
echo 'Reloading disk modules...'
modprobe ata_piix
modprobe ahci
modprobe usb_storage
Now of course the above is DOS formatted, not Linux formatted so copy and paste this into something like notepad++. Not sure if will work if directly pasted into the bootdisk creator interface with DOS line-breaks.
You'll need to create your USB flash drive root.gz again, but after booting up you should see the text "Unloading Disk Modules" and "Reloading Disk Modules" which shows that the script it executing.