I know it has been a while but to add some info. When I remap the keys for moving through my game lists (Wheel) in the Game Ex Evolution wizard the mapping works. I have a 5th joystick on my 4 player iPac set up to move around in the Game Ex FE and select games. I have this working in Game Ex arcade and it is very useful. When I map the keys using the wizard the correct bindings show up. For example up on the stick = [F6]. The problem is when I use the stick in Game Ex Evolution it scrolls through the layout options, it changes from left wheel to right wheel block list to vertical list as if I am using the little layout menu.
So here is what I found to cause the problem. The Wizard shows the "advance keyboard input" controls option and it can be disabled both in the wizard and the .ini file. The .ini file has a line to enable and disable. The wording in the .ini file seems a little different than the wizard but it's followed by a true/false in the ini and the has yes/no in the wizard. I think the problem is that if you select to turn either off in either location the group of inputs is still together in the .ini list. This leaves the inability to shut off the advance keyboard controls. In my case this caused duplicate key mappings. I had Keys like F8 handling 2 controls. So i needed to blank out the controls that I was not using or remove the duplicates with other mappings to my C-Panel.
You just can't have duplicate mappings whether or not you are using advanced keyboard inputs. It would be cool to be able to just disable advance controls and not have them contain default values and go blank in the ini.