After months of troubleshooting and scratching my head, I know why certain cores that were working on 1.0.0.3 do not work on 1.2.x.
The problem is the Rewind feature. I shut it off and now no more crashes at boot, but I also lose this handy feature. I haven’t tested all cores, but 2 cores that are affected are: Picodrive (when playing Sega CD only) and FB Alpha.
The problem is not in the cores, but Retroarch.exe itself since if I replace the .exe with 1.0.0.3 and leave everything else the same, no more crashes.