I use a RetroPie 2.6 image on a RPi 2, Raspbian is up-to-date including the latest firmware, I do not use rpi-update. Freqs are 1000/500/500 with heatsinks applied. Two WiiMote+Classic Controllers are connected via Bluetooth Dongle. (Both controllers work fine in RetroArch, e.g. we played Secret of Mana PocketSNES for hours.)
But 1.1 PCSX-ReARMed r22 has strange issues. Some Games like Mega Man X work flawlessly with Controller and are not affected. But Crash Bandicoot does accept controller input only, when no BIOS is present (warning appears). As soon as I put any PSX BIOS into the BIOS folder, no input is accepted anymore. The hotkey RetroArch menu still works, the input settings still are the same.
Do I have to play without bios? Or try more versions? I tried SCPH 7502, 7003, 5502, 1001, 1000.