Since you can see that the buttons work when using jstest, we can be sure that the driver and hardware wiring is working. That is good!

I suspect that EmulationStation needs to be configured for the ControlBlock controllers: You can either remove the ES config file from the commands line (sudo rm /opt/retropie/configs/all/emulationstation\es_input.cfg) or you can re-configure the input from within EmulationStation from the menu.