OK, a wierd and wacky theory!
Try patching it with
this +23 Trainer using either Pete's CDR Plugin's PPF Ability or just patch an ISO using PPF-o-Matic!
From what I've been told, these trainers use their own boot sequence, and basically overwrite the original one! As your problem is happening on startup, *shrug* it may just work
Everything is worth a go eh?