I use the same controller, and it works fine for me, so I don't know what to tell ya. Sorry I wasn't of much help.

Ok, the only other thing I can think of is that if you're launching the game, and you get to the screen where it shows you the keyboard commands (after the Squaresoft screen), the controller doesn't work on that screen for some reason, so you have to press x to get past that and to the main game menu. From there the controller should work.

So, turn on controller, launch game from the game launcher, wait until you get to the "keyboard" screen and hit x to get past that.

Also you can check to see if the game recognizes your controller by hitting the settings tab in the game launcher. If the "controller" tab is greyed out, then the game isn't playing nice with it.

if you're using a wireless controller, make sure that it's turned on before you launch the game. Other than that I don't know what to tell ya

Sorry, can't help you with that, as my knowledge of CE is rudimentary at best. You've already taken it further than I would have known how to. Hopefully someone with more experience with the program will be able to help you out.

Not sure if it will work, but have you tried using the speedhack option in cheatengine? It's not perfect, as you'll have to alt tab to start and stop it, but it could be useful. I would test it out to see if it works, but I can't even get the game to launch properly anymore after playing for ~24 hours, lol.

Based on the quality of your FF work, I would love to see what you've done with other games.