I tried with TLOZ: Phantom Hourglass/Spirit Tracks, Tingle's Balloon Fight, The World Ends With You, Alice in Wonderland and Pokémon Diamond. You know if this games works for other people?
Works just fine for me with those games (aside from Alice in Wonderland, I don't have that tile so I haven't tried it) and with an R4i Gold. Maybe its your micro sd card in your flashcard? Have you tried another micro sd card?