Another cool video! From the HMI, your encoder readings seemed right when operating in manual? Or were the readings sporadic/random from there? Or was it still counting up when going one direction and counting down when going the other but the zero was no longer accurate? Which was then still sending the wrong information for the arm?
No, when operating in manual, it was showing position of the arm, not were it should have been, sometimes going to 0 position out of the blue. Forgot to mention in video, when the arm was zeroed with upper limit switch, upon testing when it was showing max move done , arm at that point was only half way, hence it was clear, something was going wrong with my count.