Okay, so I've read some 25 or so pages of this thread and I can't finish it. So I figured I'll just post what I have here. I heard there's a .sav file uploaded here? It's like, a normal .sav, nothing on it. So I downloaded it and put it on my CycloDS. I renamed it to the same name as my Legend of Zelda Spirit Tracks patched ROM, and booted it up. Didn't get a Xenophobia logo, still has the starting animation. Before I used that .sav file, I tested the save feature by creating a new profile, then before starting it, I'd restart the DS via soft reset and go back in. Previously, it did as everyone said, treated it as if it was blank, a new game. Now, however, it doesn't do the "Creating new save file" thing anymore. I'm not totally sure where I got it from anymore though; if you people want, I could delete my profile (since I haven't done anything on it) and upload the .sav somewhere, and post it here.
That is, if someone hasn't already done that.