How many miles are on the X3?
You might want to check the Tension Strut in the front suspension.
Some have said that when this bushing starts to fail it feels similar to warped rotors.
Tension Strut ( also called Thrust Arm ) ( also called a Lower Control Arm Front ). This controls the lateral movement of the front wheel.
It's part #8 on the link below.
The rubber bushing on this part can deteriorate and cause a clunking at brakes. Although you would also hear a clunk over bumps and maybe while accelerating. It's a common problem on e39 BMW's too, which have a similar suspension design.
I'd climb under the X3 ( don't need to jack it up ) and grab this Thrust Arm and try to replicate the noise.
Last edited by mlukas161; 01-24-2013 at 08:02 AM.