Simon Bradley may know more than I because I use an original DVD game with larger TOC to boot the backup DVD game. AR2 doesn't figure anywhere. I'm slightly confused as to your predicament.

Exactly which Modchip do you have and does it boot CD PS2 backups OK with GS2?

Finally if it is a GS question, then if you search the Forum I think you'll find v1.7 is solid. You can download 1.7 from that nice site, I believe and then use 1.9 to boot it in and then you go from there. No guarantees - but I can use PAL DVD Region X original to boot JAP DVD Region X backup on my JAP PS2!!