I've used my controller to try play PS1 games and PS2 games and I don't get any problem like this.
Do you have this problem when playing "Summoner A Goddess Reborn" with your keyboard?
Yes I get it with keyboard as well. Do you think it might be because the game is running to fast.
Too fast? How fast is the game running?
It could be a controller emulation problem though. I think there are different odd gc controller modes.
The game normally runs at 45-50 fps but in the menus it runs at 60 and it says 100%. I just tried limiting the fps to 50, 40 ,30 and 20 and they are all the same.