If your flashcart keeps any configuration files on the SD card, then delete those... When you boot up your flashcart it will load up default setting, meaning no custom skins...
You can also try the switching thing like Zombie says, but I'm guessing if you haven't figured out how the configuration setting work, chances are you're not smart enough to switch a few files around...
And a last resort, just like Zombie's 2nd suggestion, but sure to work, is backup your games/saves/ect, format, and move them back over, excluding the config folder of course.