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So when ever I get hit by anything my controller most of the time will vibrate for even minutes until I press main menu or just leave it to vibrate.
Other than that it works fine, any help will be much appreciated.
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You could try editing the options.txt file in %appdata%\Trine2. Search this line:

setOption(inputModule, "IgnoreWonderingXInputDevices", false)
and change it:

setOption(inputModule, "IgnoreWonderingXInputDevices", true)
Then save and launch the game.