Without seeing your ctrlr, cfg, and ini files, and me not knowing LEDWiz config, it's hard to tell, but I'll list a couple easy ones.
1) In the ctrlr file, is the neogeo inputs before the default (if there is a default)? Default needs to be first, and neogeo after, then game specific after that.
2) Do you have any cfg files with remaps? Cfg files will over ride ctrlr file maps. Yes, default.cfg will over ride ctrlr file's system name=neogeo.
3) Does mame.ini include ctrlr yourctrlrfilename? If yes, do you have any system or game specific ini files also? These would over ride the mame.ini file (assuming defaults for readconfig) if the option is included within them. (Hint: if you make sub ini files for special settings, include only the lines that differ from the main mame.ini file, so changes in the mame.ini file take effect without editing the sub ini's too.)