@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?
3.4 fresh install
It’s weird, they are hit or miss on connecting from boot up. But once booted, and still disco’d, they will connect when woken.
And once they are connected, if I power them off and back on (mid game, for example), they connect right away.