I'm fairly sure that as far back as I can remember, if you press 'tab' and go into 'analog controls' there are options for reversing x and y axis.
I had tried that, but it didn't work for my trackball. It did work for my 49-way.... I think... hell, I can't remember now if I tried that or not, but it didn't work for my trackball.
You are right. Old versions did not support splitable axes. But they allowed you to invert the axis, like he was asking.
[TAB] menu - Analog Controls - Track Y Reverse = On
I'll go check it out again, but there weren't any settings for "track". I think it said "joystick axis reverse" or something like that. But I'll poke around and see what .55 has to offer me in that menu