so, you are using mameui with mala? most people running a front end like mala run the command line version of mame...
JustMichael got it right, you check those settings in those files and you should get your mouse working. when you say nothing works in mala, do the buttons work? did you configure mala to use the proper inputs? x-arcade units map joystick1 to the number pad arrow keys, instead of the standard arrow keys. try toggling your numlock button to see if that makes a difference.