I seem to have an issue with this sometimes. When i try to boot one backup that i have it wont load when the HDD is in. Is there a way i can bypass the HDD or have the system load up first. I just use the HDD to store all the PS2 saves I dont use. Saves me from buying a bunch of memory cards.
maybe I'm miss reading what your saying, but the MI only boots to the HDD when set (or button induced) to boot in Dev mode. change your settings to normal boot rather then booting the Dev elf file, it'll then boot directly to the CD/DVD drive instead. kc