Backup tool 3in1

After I turn off the DS (after its done copying the save to NOR) I start the app again and it won't let me save the file to the memory stick.
I'm quite sure the problem isn't with my NOR, I can play a game after I reboot my DS and can play without slot-1 (starting the game from the DS's menu)
I used an unpateched Super Mario Advance 2 (Super Mario World) game, so it said my save is corrupt so I couldn't play it.
The game I tried to back its save was Pokemon Platinum.

..I seem to have a hard time understanding this so let's be safe and do a reformat of the micro sd card (backing up your files of course) and see...So what is the problem, you mentioned ds AND gba games, the 3 in 1 back up tool only works on ds games...and what's this about patching?Please clear this up as I use this program regulary, sav and game dumping.