The 1400 puts in 1.25 lbs of chlorine per day so given your settings and run time that is over 3.5 ppm per day of chlorine is added to your pool. Given your CYA level, you should be at a much higher CL ppm than you are. I suspect there is a problem with your cell or controller.

Try and test the water right out of a return inlet to see if there is significant CL generated when the unit is on. Then get on the phone with a Jandy tech to see if they have any suggestions.