Thank you self_slaughter, that's probably the issue (restoring but not refreshing). I'll look in that direction.
@casey bandy:
I think the error for Baten Kaitos is perfectly normal, it means that there's no cheatcode for that game on geckocodes (the place where the cheats are downloaded from)
http://geckocodes.org/index.php?chid=G&r=*&l=b
List of games starting with "B" : only 2, and no baten Kaitos here.
Though, there's no Fire Emblem either...
all gamecube games
If you know where to get the gct or the txt, you can add the file yourself into your SD card.
rename the file to GKBEAF.txt or GKBEAF.gct
Put the txt into sd:/txtcodes folder, or the gct into sd:/codes folder.
if you add the txt, you will have to select the codes you want to enable, and generate the gct from the Ocarina menu. don't forget to enable the ocarina option too.
If you add the gct, you only need to enable ocarina option to apply all the cheats inside the gct file.
You don't need the sneek folder or the kenobigc.bin file anymore. it's now included inside nintendont.
About your controller :
you want 2 controllers to be assigned to the same player?
I don't know if it's possible nor how nintendont manage the controllers, sorry. You'll have to ask in nintendont thread about the controller's order.
About the HDD : yes you can run everything from the HDD, you don't need an SD card.
put everything on the same partition, preferably the first one.