I use a trackball for all the games. I suggest enabling the mouse but not the lightgun if you are using just a trackball/mouse (example: mame duckhunt -mouse -nolightgun). The -lightgun option should work with a mouse just as well as a lightgun, but has a coarser grid than the -mouse option (257x257 w/ -lightgun option vs. screen resolution w/ -mouse option)
BTW, greenacarina, Which games are you having problems with the mouse button? I haven't ran into this in any lightgun game yet, although I haven't played all of them. Also, I am not having problems with duck hunt or hogan's alley with my trackball. I wonder what your setup is that give you these problems....