@Firemanx Thx. Merry Christmas to you too.
It shouldn't, some scene releases are bad like unlockers or those from Suxxors that removed titlekeys by rebuilding the games with hacpac but they should work either way. At least from my experience.
First merry Christmas to you too.
Secondly just tested both editions with multimode. SEGA Mega Drive Classics and SEGA Genesis Classics and they both work fine, using them in 6.2 emunand with SX OS 2.5. So there are 2 things I can think off:
1.- Your files are wrong.
2.- You patched the game to a lower version wich won't work in case the game has dependencies from higher firmware. When that happens it gives an error at launch. That doesn't mean the game is wrong since the file will work if you update your firmware.