What program did you use to edit the desktop files? Was anything changed AFTER you put it on the flash drive?Nope. I've already avoid the issue from the beginning, no parenthesis, exclamation marks, only hyphens: Resident Evil 3 - Nemesis, Valkyrie Profile - Disc 1, etc.
Okay.
So the game that runs uses:
/bin/pcsx /usr/share/games/CLV-Z-MAMBT/Chrono_Cross_-_Disc_1.bin
While the game that doesn't run uses:
/bin/pcsx /usr/share/games/CLV-Z-NHIFM/Resident_Evil_3_-_Nemesis.bin
I also have checked the two .desktop files, other than the games names, they are all identical.