It's hard to tell from your description.
You may have installed the menu incorrectly, your microSD card could be bad, your micoSD reader might be bad, your microSD card could be corrupted (if you didn't use "safely remove harware" before removing it from your PC), you might have filled your microSD card too full, you might have too many files on the root of your microSD card (put games in a "games" folder, not on the root), you might have a bad flash cart, or you might have even fried a fake flash cart with the 1.16 menu (you should use 1.15 instead of 1.16 which has been reported to destroy some flash carts).
First try to eliminate the simple ones. Check to see if you have a fake DSTT:
http://www.ndstt.com/en/anti_fake.html
If it's fake, return it to wherever you bought it from in exchange for a real one.
If it's real and you didn't use "safely remove hardware" reformat your microSD card using the Panasonic formatter and try again. Make sure you install version 1.15 of the firmware correctly (drop the TTMENU.DAT file and TTMENU folder onto your microSD card). Make sure to put your .nds files in a "games" folder and leave plenty of free space for it to create the system files and save it needs.
If you still have problems, you might want to try it with a different card reader and/or microSD card to eliminate those possibilities. If it still doesn't work, you probably have a bad DSTT, and you'll need to return it for a working one.
-Bri