I wonder if it could be the bolt moving around in the shoe?

My SPD cleats creak quite a bit, but it's because the oval rim of the cleat is wearing against the body of the pedal (PD-M959). There is a shiny spot on the cleat and pedal where it rubs. It helps for maybe a ride if I apply grease. Probably not your issue though, as yours is happening on multiple pedals.