I have always had the same problem and had searched for hours without finding any solution. Perhaps it just does not work on the 3DS. However, I have tried it on my DSi and it worked perfectly.
Hopefully someone with better knowledge about this can help us out or find a workaround or solution.
Was there a specific reason why you need it? I originally tried it for Download Play signature check patching for custom New Super Mario Bros. Mario Vs. Luigi stages (the Download Play worked on my DSi, but unfortunately I kept getting a black screen whenever a course was selected; if anyone can help solve this problem too, that would be excellent).