Change the pad plugin in PCSX2 or PCSX-R from the default LilyPad to the LilyPad-SCP version.(seen how in image to the right)
Then copy over XInput1_3.dll from /bin/Win32/ to PCSX2 or PCSX-R's directory located at "C:\Program Files (x86)\PCSX2 1.2.1"(Or wherever the program directory your emulator is at).
NOT the plugins directory.
In case you are still having issues, perhaps you forgot that you still need to bind them. So switch over to the Pad 1 tab to do so.
