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PCSX2 1.4.0 is recognizing my controller just fine, and all it's inputs. The problem arises when I boot an ISO file the game itself doesn't recognize anything coming from the controller. That being said, the BIOS itself recognizes all the inputs when it's booted without a disc inserted. I can go to the browser and see memory cards, change system settings, etc.

Please post the contents of the emulog.txt file after the problem occurs. The file can be found in "My Documents\PCSX2\logs" for the installer version or in "PCSX2\logs" for the portable/binary version.

Please make sure to enclose your emulog in code tags like so (remove the empty space on the closing code tag!):
[code]
Pasted emulog goes here
[ /code]

I tried pasting it and it crashed my web browser. I can try this method, though.

https://www.dropbox.com/s/u9efsdf0b8cfnb...g.txt?dl=0