Believe it or not, it could still be something in the brake system. A lot of times, the caliper slide pins get overlooked as part of the brake job. Some techs forget to lubricate them which causes some binding and causes a clicking noise. You could also be experiencing a possible wheel bearing noise. Some other questions would be, does the frequency change with speed or does the noise happen at all times or just when you apply the brakes? Hope these areas give you a starting point. Write back if you eliminate these questions but still have the problem.