Sorry for picking up on an old topic, but this should still be relevant to Rotor 3D owners.
I have installed Rotor 3D cranksets together with Shimano bottom brackets on several bikes just to have clicking noises occur on every pedal stroke after covering a few hundred kilometers.
This is due to the fact of the diameter of the Rotor crankset axles being slightly larger than your usual Shimano crankset, which are explained in this thread - viewtopic.php?f=3&t=84516
The extra width of the crank axle creates additional stress on the bearing races in the bottom bracket, causing premature wear as the noise increases and eventually creating this clicking noise.
The solution is either to get one of Rotors own bottom brackets, or to use a fine sandpaper and very slightly sand down the axle of your crankset, but only so much that it slides into your Shimano bottom bracket with hand force.