So, I tested on both my NeoSD Pro AES and NeoSD Pro MVS, and got some interesting results. I was only able to reproduce the glitch on my MV4F, pretty consistently, and yes it only happens on the TE hack, not with the original game rom. On my MV1C with the same cartridge, and on my AES, the glitch never shows up on the TE hack. My AES and MVS cartridges are both running the same firmware version and have all the same settings in the NeoSD menu. I ran all of the systems in AES modes. So maybe it only affects certain systems? It's bizarre.
Justin replied some more. He thinks maybe the NeoSD uses a lookup table to determine which games to apply SLOWROM to. If that's the case then it probably doesn't use the NGH number for the lookup, since you're already using the normal KOF94 NGH number for your rom. You know what, let me try renaming the rom to the normal kof94 file name and see if that does it...