I see how I was not clear. I am hardly 'detecting rotation' nor just reading an encoder in 2ms, but doing joint angles on 6DOF articulated arm and forward kinematics to ultimate position in that time. However, if you can get repeatable results with zero dropped pulses (on a 2048-50000 ppr encoder) using any of the 5-6 methods floating around the Arduino forums please let me know. I had pulses dropping out on every method I could find with only one encoder moving at about 256 pulses a second.