This probably won't add anything to the conversation but here's what happened to me today - sounds almost the same.
My older SN30 controllers were connecting via Bluetooth and in Emulation Station they would work fine. All buttons did what they were supposed to. When I tried to play a game with them the D-Pad worked BUT ABXY weren't even registering and for some reason START was acting like B. Turns out my controllers were on 3.00 Firmware. I updated them to 4.20 (looks like the SN30 Pro latest firmware is v1.34), deleted the Bluetooth entry, rebooted and then paired them again using the 8BitDo guide. Now they work exactly as they should. It was just a firmware issue for me. I didn't see it mentioned in the thread so just putting in my 2 cents. :)