John the shoe augers WILL not grind corn. They fit real loose in the shoe auger trough. They just do what the raddle chain did in your Gleaner. They just move the corn from under the concave. No way for them to grind corn. You are seeing ground corn there from under the concave.
The shoe augers are turning??? I have seen the slip clutch jaws break and the augers not turn then you will grind the heck out of the corn because the cylinder has to throw all of the corn out the top back. Check that out. It is a long shot but I have seen it happen.
I am willing to bet that the cylinder/concave clearance is still set too close. You need to really look at the cobs and see what they look like on top of the straw walkers. Also if the corn is real dry you may need to open up the concave and really push the combine faster to keep it real full. Corn rubbing on corn will shell without damage in a soft kerneled corn. I mean really push the machine. The JD 9000s are real bad about this. Most guys slow down when they see cracking shelling problems. This sometimes is the wrong thing to do. So try opening it up until you have good whole cobs. Even leaving a few kernels on the cob until you really fill up the cylinder. The push it and see if the damage goes down.
I have seen some varieties of corn that shell harder and they will have damaged kernels at the cylinder no matter what you do. Even some times a rotor machine will do it too in those varieties.