Are you using the No-Intro romset? That one seems to be the best bet for most games.
Just last night, I loaded up Batman on my Everdrive and played the first several sub-stages with no trouble. I'll try to get the checksum for you later, but it was from the No-Intro set.
PCE roms are somewhat cursed. While games from other consoles usually have a checksum in the ROM itself that makes it easy to confirm a good dump, PCE games do not, and it's likely that there are a number of bad dumps out there. I really hope that someday, there is a community effort to dump and cross check each game with multiple copies and dumpers.