@abs7 – No one should do it.
@hobbswon Try turning the controller on at different points in the boot up cycle. Make sure the pair hasnt been lost – this can happen if you hold select for 3 seconds. If you did as per the wiki/video it should have added the auto connect rule.
Can you confirm which retropie version you are running – was it from an image?
RetroPie help guides --> https://goo.gl/Yfy8kj
Please read this before asking for help --> http://goo.gl/eLErnl