Hello,
I have the same setup as you. Home made microswitch arcade stick with USB PCB to connect it. I’m having the same problem, Emulation Station detects it fine but is extremely sensitive and basically goes through the entire menu with one swipe to the left of the joystick. When I try to map the controller in RetroArch it is spammed with commands when I use the joystick but the buttons act fine.
Hope someone has a suggestion..