That's because clearing the save with the button combo in the Cubic Ninja menu doesn't delete the payload.bin stored in the save file, just the map file that triggers the exploit.
When I get bored I start looking into creating a .cia version of the homebrew loader, since, as has been said multiple times, .cia files can give themselves access to whatever SVC calls are needed to do it. The problem is, for compatibility and not having to force developers into a work around, ideally I would have to implement the hb: service port, and information on creatoing ports is non-existant at best, and I'm too lazy to log onto irc right now and ask there, let alone go through the trouble of decrypting ninjhax's payload.bin to see what it does.
