I've been intending to write up a thread featuring the MotionInJoy drivers once I felt they had matured enough.
According to the website and readme file, you have to install the latest x64 driver (this driver has changed since my previous posts i.e. no longer blog 9) and then install the vibration update on top of that driver.
Select your gamepad profile and enable rumble and then click on 'Enable Option'. After that you can close the DS3tool window. For me, the program usually crashes on exit but does seem to save my selected options. Please note that most of the gamepad profiles don't work in the x64 driver.
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Also, if you're actually using a Sixaxis gamepad, you will
not get rumble under any circumstances. Ensure vibration is turned on in FF8 by pausing the game and turning on vibration.