OK, here's the problem. The raw save is supposed to be 8kb, but the application says that it's smaller than the save area of ROM. If I convert it to 64kb with Shuny's converter and then upload it to the retail cart, all I get is a blank save in the game. Reinmoon is out of the question, because I'm using a slot 1 device...
Never mind, I tried with Eepinator now, and it worked! I guess Rudolph has to work on saving compatibility. Which reminds me, does NDS Backup Tool FTPd have better support for these saves? Does it have a tutorial, just like the WiFi version did?