I just wanted to add my experience to this thread for any one with this problem..
I am using a 64gb toshiba micro-SD card to hold my .3ds games on the gateway red card thing.. I had the whole thing formated as exfat.. It had really given me no problems for several months until I tried to use the newish cheat system thing that gateway came out with recently..
I could use the exact search feature (where you have to input a number to search for) just fine with out many problems.. But I could not use any of the other search options (signed and unsigned options) because it would instantly just say "Error" when I tried..
I read some post in this thread (I think) that said gateway only officially supports fat32, so I copied all of my data off from the micro-SD card to some hard-drive, then formated the card as fat32.. Then copied all the data back on to it (actually I had to split a few of the games before putting them back on to the card seeing as how fat32 has a ridiculous 4GB file limitation)..
After I did that, the errors went away and I can now use signed and unsigned search options..
Although there seems to be a bug I run in to some times (both with exfat and fat32) in the cheat system.. Some times when I search for cheats, the progress bar when it says "Comparing RAM dump #XX" some times goes past 100% and just continues past the screen and never seems to end even if I wait a while.. Probably a bug that gateway needs to fix I imagine..
P.S.: Don't know why in god's name gateway team chose a file-system created back in 1996 to use on their card.. If they wanted to use an unjournalled file-system, they should have used some thing like ext2.. Or just ext4 with journalling disabled.. fat32 was created back when hard-drives weren't hardly any bigger than 4GB, and no one ever thought you would have a file bigger than 4GB.. Now we have entire films and games that are way bigger than 4GB..