Humm I don't see anormal things in log files.
You can try to edit your ~/.emulationstation/es_input.cfg
file et remove this, at the end of this file :
<inputConfig type="joystick" deviceName="USB GamePad USB GamePad" deviceGUID="03000000790000007918000010010000">
<input name="a" type="button" id="1" value="1" code="289" />
<input name="b" type="button" id="2" value="1" code="290" />
<input name="down" type="hat" id="0" value="4" code="16" />
<input name="hotkey" type="axis" id="2" value="1" code="2" />
<input name="joystick1left" type="axis" id="0" value="-1" code="0" />
<input name="joystick1up" type="axis" id="1" value="-1" code="1" />
<input name="joystick2left" type="axis" id="1" value="1" code="1" />
<input name="left" type="hat" id="0" value="8" code="16" />
<input name="pagedown" type="axis" id="3" value="-1" code="5" />
<input name="pageup" type="axis" id="2" value="1" code="2" />
<input name="right" type="hat" id="0" value="2" code="16" />
<input name="select" type="axis" id="2" value="-1" code="2" />
<input name="start" type="axis" id="3" value="1" code="5" />
<input name="up" type="hat" id="0" value="1" code="16" />
<input name="x" type="button" id="8" value="1" code="296" />
</inputConfig>