Thank you for taking the time to reply, my issues are specifc to players 1 and 2 across all systems that use retroarch.
My issues are different than io2red, he does not appear to have the issues where you need to disconnect\reconnect controllers to get them to work. He is having issues with controllers 3 and 4. He makes no mention of the issue I have. Although he has not yet responded to my question of “do they work if you disconnect\reconnect while in game” he does mention in a diffrent thread that he was able to get controllers 3 and 4 working in Retropie 3.3 in PSX. So, unless he is using a diffrent core in the new 3.4 version perhaps something has changed, or the issue is mistaken.
It seems our issues are in common by the fact we use the same controller and have followed the same guide to set them up.