Talon SR LED blinks orange momentarily

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While testing some PID code discused in This Thread "PID with encoder" of our team. We had the min/max output set to -0.1 , 0.1. When driving to a set point that took some time to finish the Talon frequently stopped/started and the LED went from green-orange-green or red-orange-red depending on the directions. I looked through the talon Talon_User_Manual_1_3.pdf documentation and found that the Talon will blink Orange if Disable ( I don't believe to be the case here) , If the PWM is lost, or throttle
is within the 4% dead band. How can I isolate the possibilities? Seems that i could be possibly operation in or near the dead band?