In Everest only, pressing B registers as X in control setup, and vice-versa. This still happens on the latest version of Everest with no mods enabled. I am using a gamecube controller + adapter with steam input disabled (steam input enabled doesn't input at all in-game).
I've never had this problem running the same Celeste setup for 1000 hours. I remember having this problem a few months ago but I can't remember if/how I fixed it :|
#Wrong controls in Everest, works fine in Vanilla
rain sun
stoic hound
do you normally play on XNA? I'm surprised that can handle that controller at all