odd problem, i remember someone once having a similar problem, if it is the same problem it was caused by having 2 inputs, xpadder inputs controller keys and the game itself can use the controller (so every time you press a button on your controller it gets 1 input from the controller and 1 from xpadder),
if it is the same problem to solve the problem you could just not use xpadder, the game does work with a 360 controller without the need for xpadder (although triggers on the controller don't work so you have to configure the controls inside FF7 to what you want them to be and also the dpad doesn't work you have to use the control stick)
Or you could use custom a custom driver like "XBCD" for 360 controllers (that's what i use) which will allow you to map your controllers buttons so you can tell it to use triggers as buttons so they can be used in ff7 and you can also enable it to use the dpad instead of the control stick or you can make it so it can use both.
Hope this helps with your problem (if your problem is the same).