I have a button problem myself (could very well be a problem with the input plug-in not wxmupen64plus, I'll have to do more research. If so, I'll post this on a more appropriate thread). I was trying to get my Datel Retro Wireless Wiimote set-up, but for some reason I can set only one button at a time. For the first button, I click on one to set; it says "press a button"; I do; and the button gets set. However for the second button, again it says "press a button", but when I do nothing happens. This requires me to set one button at a time, close, and restart the program to set the next button. A bit tedious, but not a huge hassle unless I were to switch out joysticks a lot. Once I'm in the game, the buttons work fine once set.
Additionally, I have an axis problem. I can only use Axes' 0 and 1 from the input set-up (and same as the buttons, I can only set one at a time, then have to restart the program). Axes' 2, 3, 4, and 5 do not work at all. In the game itself, none of the axes' work at all (including 0 and 1, despite their working from the input set-up). I also checked to make sure it isn't a hardware problem with the joystick - I can use all the buttons and axes' fine from jscal.
When I get a chance, I will try some different joysticks, and I'll also try linking this one to mupen64plus without your front-end. That should hopefully rule out your program as a cause of the problems, and should reveal if it is just this joystick, or possibly something in my system that could be causing the odd behavior.