One thing to check is that both coils are working.
Get some kind of metallic magnetic object, like an allen key or something, and plug your guitar in. Then gently tap the slugs on each coil on the neck - it should make a loud clicking noise (so don't turn your amp up too loud :lol:) If both are working, each coil should make a noise. If one does not make the noise, then the wiring must be bad.
I don't know other than that, but I hope it helps :)