Does the .ini file need to be in a certain place? AFAI can tell it's making it in the MAME directory that's on the root drive, does it need to be somewhere else?
"mame -cc"
should generate he file in the correct location -- either the "mame\" or "mame\ini\" folder. (depending on MAME version IIRC)
If there is a "mame\ini\" folder, the mame.ini file should be in there.
Two other things to keep in mind:
1. If that type of device (mouse/trackball/spinner) isn't plugged in, MAME will not offer it as a default option.
2. If you changed any control input settings for a specific game, that will override mame.ini and defaults -- return the inputs to default settings using Enter, ESC (sets it to "none"), Enter, ESC. (resets it to default)
Scott