When using the JOG SRC command to set up an external encoder or analog input as the clock source for a JOG move, it is important to remember that only "positive direction pulses" or "increasing counts" are used as clock pulses. Any pulses occuring in the negative direction will be ignored.
If it is desired to keep track of negative direction pulses, use a software ratchet (RATCH) in Mode 3 to buffer the negative counts.
Software ratchets are sources that can ignore, negate, or buffer both positive and negative pulses. When a ratchet is set up for buffering, pulses in the buffering direction are added to an internal count instead of causing the ratchet output to change. Pulses in the normal direction are first used to unbuffer previously buffered pulses. When there are no more pulses to unbuffer, the ratchet tracks normally.
This is true of the MASTER SRC command, as well. You cannot back up a trajectory path, or a jog path by sending in decreasing count clock pulses.