i had exactly the same problem as you when i was setting up my current mame setup i am using a playstation dualshock2 controller via 'psx to usb' adapter, but noticed after setting up the controller in mame, then later if i ran mame with the adapter unplugged, all my controller/buttons config disappeared (and didnt return if i ran mame again with the adapter plugged in again). the only solution i came up with was to set up the controller (and keyboard etc) how i wanted, then quit mame, and then set the default.cfg file to read only. then mame wont be able to touch the file again if you happen to run mame with your controller unplugged in the future
ps. i agree with what you say, it would be better if mame checked to see if the controller is active, and if it isnt, then simply dont display it in the config menu (rather than actually re-write config files)
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