Make sure you format your microSD card using the Panasonic formatter.
Make sure you put all your games and save files in a "games" folder and not on the root of your microSD card.
Make sure you leave some free space on your microSD card for system files and save files.
Always use "safely remove hardware" before removing your microSD card from your PC.
Check to see if you have a fake DSTT. If you have a fake, you may need to recover it, and make sure to put the patched firmware on it (the patched version has the fake-killer code disabled). You can find some programs here to check to see if you have a fake, to recover a fake, and there is a patched version of the firmware as well: http://gbatemp.net/index.php?download=4086