Do you have full screen turned off in game?
That's the only problem I can think of for it. Or maybe your DSfix is just messed up or something I don't know.
Also why do you want to play Recettear with a controller so bad?
Also also did you send me a steam message? There is a chat window open for you but nothing was in it. It was weirding me out so I just closed it.
Thanks Naro, you were an awesome help.