You may need to uncomment the line at the top of your mame.ini file that points to the path of your ini folder. Like so:
### mame.ini ###
### Frontend Related ###
clones 1
### Windows path and directory options ###
rompath roms
samplepath samples
inipath ini
cfg_directory cfg
nvram_directory nvram
memcard_directory memcard
input_directory inp
hiscore_directory hi
state_directory sta
artwork_directory artwork
snapshot_directory snap
diff_directory diff
ctrlr_directory ctrlr
cheat_file cheat.dat
history_file history.dat
mameinfo_file mameinfo.dat
It will then look in the .\mame\ini folder for game specifc setting. You do not need the entire contents of the mame.ini file in the game specific ini files. You only need the line that are not the same as the settings in the mame.ini file.
Good Luck,
John