I am having this same issue with my f310 game pad and Legend of Mana on the psx. I have tried everything including setting all 8 pads to analog but to no avail. The switch on the back of thr f310 is set to X-Input mode, so the analog should work. What am I doing wrong? I really want to play this game on my retropie.
I finally figured it out. After doing the above, I had to save a config file for this game and then hit select and the B-button to reset the game while my settings were in effect. After it reset, I was able to use the controller. I was about to go crazy trying to solve this.