Sorry for not responding to the issues on GitHub; was busy with life and college. I was planning on getting to them eventually, just... never did.
IIRC, the button values for the port are hard-coded, so changing them around likely won't fix anything. My settings file has the exact same values for keyboard and controller as yours does. Besides, I had heard reports of issues with regards to input and getting stuck on the title screen; this sounds like a related issue. Would you happen to be using the Android .rsdk file?
Currently prioritizing the Mania port, however, I might take a second look at the input code once I've got this other stuff out of the way. Also, to my knowledge, RSDKv5 has backwards compatibility with previous Retro Engine versions, so I may just end up using that as a basis for future CD releases anyways.