So I was messing around today and I found out that in order to to use the HDD support in Codebreaker you need the following
1. An official 40GB sony PS2 HDD
2. If you don't have the above you need a ATAD patching modchip.
otherwise the intial created 128MB partition comes out currupt, the BSOD you see until the next time you launch Codebreaker, I verified this on a PAL V9 with an unofficial 10GB HDD using the HDD OSD hack
it shows the partition as currupt and has purple icon on the HDD OSD screen.
You maybe able to continue the ATAD patch of the OSD Hack onto launched apps through the HDD OSD though if they don't reset the IOP ie: launch a Codebreaker ELF off the HDD OSD to have HDD support on an unofficial HDD ;-) keep in mind though the HDD OSD hack performs a IOP reset of it's own and terminates FMCB so you can't launch ELF's using FMCB's methods as it uses the normal OSD screen only with HDD, Keyboard / Mouse support added.
I'm still trying to find out how you launch apps off the HDD OSD without using a game with HDD support via dnasload.elf though, everytime I tried I got presented with wrong disc or insert disc although the ELF I used wasn't a disc signed KELF that might have been my error.