I've got a bike with a Shimano Deore mechanical disc caliper in front. I recently laced up a wheel around a Shimano Dynamo hub (to power a light on my commute). The dynamo hub takes a centerlock style rotor, whereas my old hub had the 6 bolt style.
The new rotor is the same diameter (160mm) and I've adjusted the caliper to accommodate the slightly thicker CL rotor. Things work basically ok, but I just don't have the same stopping power that I did on the old 6 bolt rotor.
I did notice on the new CL rotor it said "use only resin pads". I'm fairly sure my deore caliper has metallic pads (are those materials interchangeable?). I'm hoping I just need to monkey around with my brake setup and can remedy things.
How long have you been riding on the new rotor. As brakes pads need to "bed" into the rotor. It will take abit to get full stopping power even on new pads and rotors. Rotors will have small grooves and inperfections as will used rotors more so as the brake pad has mated to the old rotor. give it some time and it will probably get better.