Having the analog joystick active is what is causing the problems with the Trackball as you suspected. Since all of the games I am playing with the GP-WIZ 49way joystick use digital inputs for joystick directions, do you know if JOYtoKEY also translates the joystick directions into keyboard strokes (like left arrow, right arrow)? I have tried this program and it works pretty well on the buttons, but I didn't try to map the joystick movements yet. Also, I loaded up RBJoy, but it was at 3 in the morning and it wasn't apparent how to map the modifier keys like CTL, ALT, SPACE.
Mark,
Specifically, what games are not responding with the trackball when you disable the analog axis inputs? (I would like to do some testing.)
I had a similar problem with trackball games and an analog joystick using the gameport. I blamed it on the archaic gameport interface. The solution for me was to either disable joystick input or unplug the joystick, but I think that would disable all the buttons on the GPWiz49. I don't have a GPWiz49, but I think I could model what's happening with a USB PC joystick and a mouse.
Also - to disable the axis - are you setting it to NONE? Try setting it to R or E or some other seldom used keyboard key. I think it is possible that MAME assigns the mouse to that input and if it is set to NONE, the mouse is disabled. I don't know if it's still true, but you didn't used to be able to change mouse assignments. For example, in Ikari, I can go into the inputs menu and assign P1B1 to A/D X-Axis + and moving the joystick left would fire a shot, but I couldn't spin the mouse and have a left mouse spin fire a shot. Even with MAME Analog Plus - I could change which mouse or axis made the player spin, but I couldn't make the mouse control a different function.
As far as an easy setup fix, MAME has changed controller schemes about 3 times in the last two dozen revisions and I haven't kept up. There used to be a trackball.ini or mouse.ini or something setting that you could use for all games using the mouse. There probably is still something similar. Try visiting EasyEmu.