Right-click PES2016.exe , go to Properties > Compatibility, and set it to run for Windows 7.
Note: If disabling it doesn't work, try "Enable Steam Input" and use Steam’s Big Picture Mode to map the keys to a standard Xbox configuration. Step 3: Use X360CE (The "Link" Fix)
Occasionally, aggressive anti-virus software blocks the Settings.exe from writing to the configuration file. Add the game folder to your exceptions list.
Unlike modern titles where you change controls in-game, PES 2016 requires you to map your hardware externally.