I had gotten an incomplete autopilot panel back out I had sitting on the backburner for a while and started wiring it up. Initially everything was going good. Then for some reason there was no response at all in mobiflight or on the mega board I had it plugged up to (that little orange flashing light when you press a button). Naturally I thought I may have a bad connection somewhere and checked my work. Everything looked good. I got fed up with it and went to try out my older completed panels, they’re not working either. Mobiflight recognizes the arduinos just fine but that light is not flashing and there is no response whatsoever to inputs. I reinstalled mobiflight and it didn’t help.
Well I got my old board working, for some reason the configs were set up toward the mega I’m using for my autopilot panel. Don’t know how that happened. This one I’m working on now still isn’t working though. I’m gonna triple check my connections I guess.
EDIT: Traced by ground all the way through it’s solid. Pushbuttons started working again, idk what to think of that. I forgot to connect the 5v to my encoders though which explains why they aren’t working. I’ll solder that up real quick and get back.
EDIT: I’ve got everything wired up correctly now. Everything works but the encoders. IDK what’s going on. They all have 5v, gnd and their own pins.
EDIT: Looks like I’ve found the problem. I didn’t break anything like I thought I did thankfully. The encoders need their own ground directly to the arduino. I had all the grounds connected to each other to terminate at one ground pin on the arduino.
You may have more luck asking questions on the Mobiflight Discord. We are friendly folks over there 
There are 4 encoder types to choose from in the Arduino pin setup. If you aren’t getting a 1:1 ratio, then you’ve selected the wrong one.