I think the issue may be due to the length of wire from guitar input to ground or elsewhere. The input is not directly attached to the chassis, and a ground wire is run to it instead.
Discussion
Long ground runs from input jack to chassis can induce hum via magnetic pickup or ground loops. Direct-mount the jack to chassis if possible—it's the gold standard for clean signal. If not, twist/shield that wire and keep it <6 inches. Test it.
Could that cause the issue I've explained?