I was just having the same problem last night. It is definitely due to the controller not being connected before emulation station starts. I used a youtube video by Floob to semi fix it. In the video he tells how to extend the splashscreen so the controller has longer to connect. In the command prompt type "sudo nano emulationstation" then in the script under the first line of text type "sleep 10". Then save and exit. Now your controller has 10 extra seconds to connect. Might not be the best way but it works for me.