Thanks for your update. I just came back and also tried again to apply when I left, with the following result.
IO called the IT rep for me (that's a contractor, not a government official). IT rep tried to blame it on the passport: Too shiny/reflecting surface. I said that can't be, as the manual counters, and the auto-channels in Europe, have no problem reading it. They said that those use a different system. I said, you see what your problem is. Your system simply is not good enough. IO filed an official complaint for me.
I encourage everybody to ask the IO to call IT, and ask the IT when it will be fixed. As PR holders, we have a right to use the system and they - the contractor - denies it to us, so we have to wait in line for an average of 30-60 minutes. The IT rep can't do anything, but you can ask them to call their supervisor, 24 hours a day, so that it trickles up that there is a problem. You see, there aren't many German PR holders who want to use the auto-channel, and if it isn't brought to their attention often, they - the contractor - simply won't care to fix it.
An official complaint is also good, maybe someone at Immigration in CW will notice and talk to the contractor.