Don't know what to tell you. Whenever I have issues, I switch ripping and converting programs. I've gotten some really problematic games to work all the way through (such as DQVII). Over the past few years, I must have converted FFVII 3 or 4 times before I finally dedicated enough time to really beating it, and that game was never one of the tough ones to get working for me.
If multiple rips/conversions all fail in the same place, then I'm likely to blame the discs. The rip/conversion process is particularly sensitive to flaws. Flaws that a normal Playstation console / PC optical drive might just overcome without issue.
:/
Edit - You've verified that your POPSLoader setup is working, right? I mean, with other games?