@Chris Annin Thanks, that solves the problem! I think for some reason the two pins are flipped for the CUI encoder compared to the new encoder. A side note, I found the wiring diagram on page 221 of the AR4 manual really confusing. The color of the cables and the numbering of each wire is completely different than page 250. I have to trace each wire by number, not by color.

Hi Chris, I tried to disable encoder for J1 and it works fine. The same hardware works fine with the AR3 software. I enabled J1 encoder and tried incremental jogging by 10 degrees again, I noticed that the angle slightly drifted by about 0.1 degrees everytime (fixed value). May be a rounding error in the software?

I have been testing AR4 software on AR3, the calibration works fine for me. I was able to adjust offsets for each joint. One thing I noticed is the angle from limit switch to 0 is not adjusted with the offset. So if I jog the robot to the extreme position, the limit switch is pressed too hard. Another thing that prevents me from further testing is Joint 1 gives me a 'collision or motor error' if I jog it slightly.

I also found out that the Arduino and Teensy share a common ground since both are connected to the PC. Could this be an issue? I think according to the manual these two microcontrollers should NOT share a common ground.

To follow up, it seems the above only happens when I use a 5V external power supply (which is needed to control servos). If I power the encoder and limit switches with teensy +5V, everything works fine when stepper motors are enabled; If I power a servo with external +5V and common ground to teensy, the encoder values keep increasing. Does anyone use an external +5V power supply for servos? Do you get good encoder readings? Thanks.