Same problem, can pair the PS3 controller just fine, Emulation Station works fine, SNES emulator works proper with controller, NEOGEO doesn’t respond to any input (FBA). Even the keyboard does not respond to insert coin (or anything).
Clean Flashed, same problem. Install Retropie 2.6, working controller. looks like input is blocked on 3.0 with PS3 controller (bluetooth). Changed hotkeys, configs and what not, but no joy