This just happened to me a few weeks ago. My core was half plugged and had to be replaced, and then I found this problem:
That arm is powered by a small electric motor inside the programmer. If your system is working correctly and everything is up to operating temprature, you can turn the temp control on the dash up and down and hear the little motor running and see the arm moving accordingly. The engine does not have to be running but the key has to be on.
I disassembled my programmer and found that the little motor was bad. I replaced it, reassembled it and it worked great.
I was going to take some pics of the repair but I did not. It is crazy that just a few weeks later I need them.