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When I use my Logitech GamePad and its right analog stick, I find that the cursor for windows is affected. That is, it moves the cursor around just as if I were using my mouse and does not stick to the boundaries of PCSX2. I have tried various controller plugins, and the problem persists. Additionally, I am not sure, however the L2 and R2 buttons refuse to be assigned when doing the configuration in lillypad. The controller does show up in the device list and does work properly in game with the exception of the aforementioned problems. Just a side note, I haven't really gotten to a point in the game (Final Fantasy XII) where I can use the R1/2 or L1/2 buttons so I am not sure if it is a problem that I can not assign it. Thank you for your help.

Maybe you have something configured horribly wrong or maybe another app is interfering, would help if you show us your lilypad configuration. Also make sure you set both first and second controller plugins to the same one just in case.