The Codebreaker disk itself wasn't meant to work with any HD. Not to mention, the newer disks don't like anything being plugged into any of your USB drives while loading.
If you're using the elf, you need to use the one that is set up to work with HD. Also note, that the elf is just like the disk, it doesn't like having anything plugged into your USB drives while loading. The trick to get around this is to actually have the elf file on your FMCB card and add it to your PS2 boot menu. Load your cheats for your game and then it go to uLaunch. From there, plug in your HD and select it from your uLaunch menu. Select your game on your HD and you'll be good to go.