Well, first and foremost, the differences came into play when SNK started to deivse protectons for their Neo-Geo arcade boards so that they would be harder to pirate (this started with KOF99 and Garou). So the emulators at that time only had sets that didn't have any kind of protection. They couldn't run the newer games because they couldn't emulate the protection. Eventually, people circumvented the protections (or knew how to make code the emulators such a way that the protections would also be emulated - on the fly decryption). The emulators that were actively being worked on (Nebula, Kawaks MAME) quickly implemented the decryption routines into their respective code, but emulators like NeoRAGEx that didn't have virtually any development going on had to resort to hacking individual files in the romset. A further problem for NRX was that it could only handle files up to a certain size per file and it could anly work with romsets that had their filesnames follow a different pattern. Other emulators had strict rules of how they handle the files inside a romset (decrypting encrypted data, perfectly matching CRC values, size in hex, etc.), and could work with files of all sizes as long as the code was adjusted accordingly. NRX had to result in hacking Neo-Geo program code to remove the encryption but also keep all the filesizes between their size boundaries. As the files started to change, they had to be treated as completely different romsets.