The newer builds for the Pi2 use lr-mednafen-pce as the default pcengine emulator but the controls are not mapped correctly. Using my SNES controller as an example the two pcengine buttons get mapped to Y and B.
If you load the pcengine roms with the lr-mednafen-pce-fast emulator then the two pcengine buttons are mapped correctly to the A and B buttons.
Not sure of the differences between the two emulators but thought I would bring it up.
That is good to know. BTW you should be able to remap the core controls now under the quick menu in the rgui (called core input remapping) so that they match the other PC engine without needing to change your retroarch.cfg
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