huntereb, i guess you started playing your pokemon game on emuNAND or on sysNAND 4.x right?
laurorual said he/she is unable to play the game on emuNAND classic mode. This implies he7she started the game on sysNAND higher than 4.x. At some point Nintendo changed the encryption keys thus making you either unable to play your pokemon edition on consoles with sysNAND 4.x but able to play on any console using sysNAND higher than 4.x, or you did the opposite and made yourself unable to play on the newer firmware versions. then you may be able to dump your own game and continue the game where you left of in emuNAND. But if you started playing on non-4.x sysNAND there is no way to get your rom with your save working in emuNAND because of the encryption keys. The same applies to the physical cartrodge when using classic mode.
I started playing my Pokemon Y on sysNAND 7.2, and despite being able to flash back and forth between firmware versions, i cannot play my game in emuNAND 7.2 classic mode (cartridge) or as a rom in emuNAND 7.2 gateway mode. This remained unchanged after updating gateway from 2.2 to 2.3b and emuNAND from 7.2 to 8.1.
But i could also be terribly wrong of course, so if you found a way, please tell me / us. Would save me lots of firmware flashing
EDIT: got ninja´d... gamesquest said the very same, just much more sleek and swift instead of wall of text.
quantumboy: i dont understand that much about the functionality, but having the correct encryption keys would require you to boot right into a NAND version higher than 4.x. That either disables gateway alltogether because of being unable to exploit the NDS user settings, or is simply impossible because you cannot boot directly into emuNAND, and as far as i understood, those keys are generated when powering on your 3DS.
EDIT2: Scratch that and read what gamesquest wrote.. again ^^