Same problem with new installation.
I have a GamePI20 and can't use it with 4.7.x version (driver/module not support the Kernel version). I use the 4.6 instead. All working great, the GPIO controller work fine in emulator and ES, but under dos-like menu (Raspbian, emu config, packages updates, etc..) only the Pad key Up don't made the right action (tab over bottom buttons). Is do not happen on SNES clone USB controller.

@mrvanes , I follow the request of @Melvin-FoX , you have updated, ok, but what are updated ? Kernel ? Setup-script ? I don't want OS upgrade, because if the kernel is updated, the GamePI20 stop working (no LCD, no pad). But if you have updated all, I guest you don't know the lib or other thing that fix exactly .

(sorry for my poor English)

The behavior I'm seeing now a days is consistent between EmulationStation and the RetroPie-Setup Script. The big outlier for me is the Raspi-Config menu being the opposite of everything else. Has anyone discovered a way to swap the confirm/cancel button behavior for Raspi-Config?