When using a auto sell chest many players including myself have noticed it tends to cut sales short about 50% per item was this a intentional feature or just something that ended up happening and wasn't called to attention or fixed?
My auto sell chest has been working properly all season. May I ask if your hopper is constantly full?
If your hopper is constantly full, the efficiency transferring to auto sell chest will slow down and could cause a full hopper line. Maybe try tweaking your hopper management, hopefully it could work. I personally use mine cart hoppers for most of my spawners instead of chunk hoppers (crop or mob hoppers) as the transfer rate is faster in my opinion.