I have the same problem. I'm running a 4.2U neogamma r8 beta 15 ios249 Rev19. And after installing the custom ios 249 base 37 v38** i cnt load any games that were working before from off of my sd card which i load my games on from WBFS manger.
Yeah it works great but it's the obvious Ds factor you loose from it it's not like playing atari games on atari because Nintendo actually use to give a reason to buy their hardware
I just like game consoles how they were intended to play if they have a unique enough reason to buy them anything else yeah just download emulation for it