I had the same problem and I used another micro sd and it worked, check below :
1) Copy the mset cia for your region to the INTERNAL microSD of your N3DS.
2) Get a spare microSD and format it.
3) Copy launcher.dat to the root of both the new microSD and the one you're using in your N3DS.
4) Copy DevMenu.3ds to the NEW microSD. Make sure it's DevMenu and not BigBlueMenu. If it says Title Manager it won't work!
5) Insert the new microSD into your N3DS internal card slot.
6) Boot your N3DS, wait for it to create the necessary files on your microSD.
7) Start the gateway launcher by using Zelda or Cubic Ninja.
8) Select "Install NVRam" and let it finish.
9) Insert your Gateway (without any microSD!) into your N3DS, boot Gateway mode.
10) Once in sysNAND, remove the new microSD from your N3DS and replace it with the microSD you use for emuNAND.
11) Insert the new microSD into your Gateway card and put it in your N3DS.
12) Press select and mount DevMenu and start it.
13) Import the mset CIA for your region.
14) Reboot
15) Profit!
This is from a member of this forum, can't remember his name sorry