Mednafen now can emulate the Neo Geo Pocket(Color) too, at least on small endian platforms. For more changes see http://mednafen.com/ Renaming the ebuild worked fine for me.
Up to 0.6.5 now, works fine for me too with renaming (on x86.) Author states it fixes NGPC emulation on PPC, among other bugfixes.
Fixed, thanks.