Hi,
I use non-mame default keys too.
But I changed them within mame for all roms using the mame interface.
When you press tab during a game, it gives you the option to set controls for 'general' as well as 'this game only'.
Just choose the general option, and your changes will change the mame defaults.
If you have already set up individual controls for most of your games, then you may have to delete the config. files first so that the games use the (new) default settings.
Hope this works. Sorry, I've not heard of mameset.exe.