Are both cards at the highest firmware? At least the M3i Zero GMP-Z003 should work.I installed the cia and my iTouch 2 and M3i Zero show up on my N3DS, but it gives an error message to turn off the system when it is launched.
Nintendo introduced a anti-flashcard patch with the firmware 4.2 or something like that which checks DS cards for their savegames. Cards that didn't work with this firmware won't work with this tool.