I have the same problem, I installed the new version RetroPie_OpenELEC_Dual-Boot_v7_SS, I proceeded according to this video https://www.petrockblock.com/forums/topic/video-guide-for-ps3-wireless-controller-on-retropie-3-final/ but my PS3 gamepad works only in the menu, does not in any ROM (Megadrive, PSX, Nintendo) is not working. The previous installation Retropie 3.0 RC everything worked OK.