Sorry I misunderstood your first post then, so you have a neek2o build in a sneek folder on the root of your drive right? Your not using an older Uneek build I assume? I just tried out Castlevania Rebirth with the launch in neek2o method, the option appeared for me in the games indivdual settings page 4.
Game launched, I have return to WiiFlow on, so it returns me to WiiFlow in e-NAND, if you want to go back to real NAND afterwards you just choose "Real NAND" in the "exit to" section of the home menu. I know that tidbit of info has nothing to do with your issue, it was general info for others.