The problem is the same with 2.6 and with 3 Beta 2.
Allways after clean install.
In the first boot “No gamepads detected”.
With F4 I exit and execute retropie_setup.sh with sudo, I expand the file system and I have the same problem when I go to configure joystick.
I’m using Raspberry Pi 2.
I have a Raspberry Pi B with an older version of Retropie (summer 2014) and there is no problem with the joystick.