My copy of Persona 3 FES (NTSC-U - SLUS 21621) works fine with latest ESR. Have you tried DVD OFF version?
Do you have the same problem with the original? Does the patched backup work in an emulator?
Anyway this game has only 1 ELF file, so I doubt this is a ESR-related problem, maybe your lens is getting old, or maybe it's just a bad burn.
SCPH-90004a CB [8A] BIOS v220 // FreeMcBOOT 1.8b // ESR beta r9b DVDV Direct // Sony 8MB Memory Card
ESRPatchJAVA 0.24a // ImgBurn 18.104.22.168 // Verbatim DVD-R @ 16x // Pioneer DVR-216D