A. Encoders are set up for feedback need to make sure the pulse inputs 1 and 2 that share the same pin connections are disabled.
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Disabling these will cause the encoder values to populate when queried.
If in closed loop the watchdog timer kicks in, and these inputs are not disabled, the controller will cause erratic behavior for both motor channel inputs. Disabling the pulse inputs 1 and 2 completely will eliminate this problem.