what flashcart are you using?
I had the same problem, and I think that you haven't noticed the most frustrating issue of this game, when you finish a mission, and you return to the guild, the game will freeze if you have the cheats on. (or at least that happens to me @_@)
I don't know how to solve this, I get the same error on my r4 with woodR4 and with the r4 original fw, and with the U and EUR room.
BYW you can still use the cheats on the dungeons, but you have to test each one of your cheats to see wich one is the one that cause the plain seeds.
the cheats that I used and had no plain seeds trouble are:
exp ?x (I used 4x)
full belly
only those two, btw, you can activate the ?x money, and ?x team points (I don't remember the name), but has no sense, cause if you leave them active when you exit the dungeon and return to the guild, the game will freeze.
I trow away the game because I had to
1 save the game,
2 soft-reset and disable the cheats,
3 load again the game and return to the guild, select another mission, and enter the dungeon
4 save the game
5 soft-reset
6 enable the cheats
7 and before exit the dungeon, repeat those steeps
Some extra info: It is not a firmware issue, is something between the game and the cheat, I haven't tried with YSMenu, but I don't think it would solve this issue