@JHamz
Hmmm...check to see if your using "udev" & if not set to "udev"
RetroPie -> Configuration Editor -> Advanced Configuration -> Configure Libretro options -> all/retroarch.cfg -> input_joypad_driver (udev)
Here is what my EmulationStation mapping for my wireless X360 controller looks like:
nano /opt/retropie/configs/all/emulationstation/es_input.cfg
<inputConfig type="joystick" deviceName="Xbox 360 Wireless Receiver (XBOX)">
<input name="pageup" type="button" id="4" value="1"/>
<input name="start" type="button" id="9" value="1"/>
<input name="up" type="button" id="15" value="1"/>
<input name="a" type="button" id="0" value="1"/>
<input name="b" type="button" id="1" value="1"/>
<input name="down" type="button" id="16" value="1"/>
<input name="pagedown" type="button" id="5" value="1"/>
<input name="right" type="button" id="14" value="1"/>
<input name="x" type="button" id="2" value="1"/>
<input name="select" type="button" id="8" value="1"/>
<input name="y" type="button" id="3" value="1"/>
<input name="left" type="button" id="13" value="1"/>
</inputConfig>
Something else I read is to add a "sleep" command in the EmulationStation start script in /usr/bin/emulationstation
https://github.com/RetroPie/RetroPie-Setup/wiki/EmulationStation#es-doesnt-detect-my-controller-when-started-at-boot
Another thing I read was it can be an issue/bug in the SDL and here was the "hotfix":
http://blog.petrockblock.com/forums/topic/problems-getting-ps3-controller-to-work-properly/#post-119984