Same problem here with IPAC2 and retropie3RC.
I read somewhere that the current pifba doesn’t have the player 2 enabled on the keyboard, is it possible to activate it?
This post suggest to replace pifba emulator with another version, but i’d prefer another solution if possible:
http://blog.petrockblock.com/forums/topic/player-2-keyboard-controls-on-pifba-dont-work/