@Chillimonster I got this fixed on retropie 4.0. It needs to hex edit the driver file.
wget http://sourceforge.net/projects/hte/files/ht-source/ht-2.1.0.tar.bz2
tar -vxjf ht-2.1.0.tar.bz2
cd cd ht-2.1.0
sudo apt-get install libncurses5-dev libncursesw5-dev
./configure
sudo make
sudo make install
sudo ht /lib/modules/4.4.13+/kernel/drivers/hid/hid-dr.ko
alt + L and select replace (Use tab key go to hex)
09 30 09 33 09 32 09 31 09 34 (put in find field)
09 30 09 31 09 32 09 33 09 34 (put in replace field)
Yes to confirm. Alt + F and select save. Alt + F select exit
sudo ht /lib/modules/4.4.13-v7+/kernel/drivers/hid/hid-dr.ko
and do the same replace again
rm /home/pi/.emulationstation/es_input.cfg
reboot
Redefine controllers in ES.