The Joypad config is not straight forward, as you would expect it to be.
Each game type S11,S12,ZN1,ZN2,RZ needs to have correct buttons mapped.
this is done in the CONTROL tab in gamebase.
all s11 games must have that set in the gamebase control tab
*most other games will work ok with a default ZN1 (6) set.
even though some buttons will not be mapped.
If you look at the s11.cfg, you will see the joypad button map starts at button 9.
1-8 are not used.
so if you use s11.cfg with a zn1 game, buttons will not be configured and you will not be able to start the game or pad will seem broken.
Aqua Rush uses RZ 3 button config
with buttons in a line
x1 x2 x3
Tekken 3 uses (S12) 4 buttons like this