Just tried your app theob42, and it worked like a charm for me. (Im using Win7 64 bit)
jadder: make sure your mame.ini file points to the correct folder location for the cfg files. Here is what is in my mamepp.ini file:
rompath C:\Users\Ken\Arcade\Mame\Roms
samplepath C:\Users\Ken\Arcade\Mame\samples
inipath C:\Users\Ken\Arcade\Mame
cfg_directory C:\Users\Ken\Arcade\Mame\cfg
nvram_directory C:\Users\Ken\Arcade\Mame\nvram
memcard_directory C:\Users\Ken\Arcade\Mame\memcard
input_directory C:\Users\Ken\Arcade\Mame\inp
hiscore_directory C:\Users\Ken\Arcade\Mame\hi
state_directory C:\Users\Ken\Arcade\Mame\sta
artwork_directory C:\Users\Ken\Arcade\Mame\artwork
snapshot_directory C:\Users\Ken\Arcade\Mame\snap
diff_directory C:\Users\Ken\Arcade\Mame\diff
ctrlr_directory C:\Users\Ken\Arcade\Mame\ctrlr
cheat_file C:\Users\Ken\Arcade\Mame\cheat.dat
When I first used theob42's app, it didnt appear to work.
I got to looking around and found out mame was writing my cfg files to C:\cfg
I am using mame on this computer just to set everything up for a cab project, and I guess I havent really got in deep into the mame settings.
I went ahead and put full path to each of the above, just to make sure. Of course I will have to change it again when I transfer it to the cab.
Dont know why the standard \cfg didnt work, may be a 64 bit issue?