If you try the original, does it work perfectly fine? Kinda sounds like a software bug.
Also, I just checked and the default game profile has the weak sectors set to ignore, so I guess thats normal. Since you used the twinpak method, I assume the game is securom protected and that protection takes advantage of subs not weak sectors so I wouldnt be too concerned about the weak sectors. Also, can it be that the AOpen is just a poor sub reader? You did say it worked in the DVD-ROM.