everything is stored on the msd when it comes to the ak2/2.1/2i. if you are just swapping the msd everything would continue to work. perhaps something is corrupt on your msd. perhaps the game you are trying does not have a gameID in the cheat.db. its hard to really help you without more detailed information.
what firmware?
what revision?
what is the HWID if your acekard? (this one is really important)
what loaders (by date) are you using?
what is the rom?
did you verify the rom crc?
did you verify it is a good/clean dump?
did you verify the rom's gameID is in the cheat.db?
did you try another copy of the rom?
did you try another dump of the rom?
did you try another region of the rom?
have you used cheats on this rom while the same microSD is in the other acekard?
did you read the akaio wiki cheat section to make sure you are using the firmware correctly?
have you tried reformatting the msd?
have you tried the same files on a different msd in a different acekard? (because it could be the msd)
have you tried deleting/redownloading the cheat database?
have you tried removing optionlist.bin or OPTIONL~.BIN (a bug in the new dev kit is causing 8.3 file names)
have you tried cheats on another rom?
i can't assume you know what you are doing, so more information is needed.
-another world