I just ran into this. I updated a REV13A (it still works) TIU and remote and had the same thing happen. I thought I would try what I read in this thread and it happened. The engine was a PS3 UP 0-6-0 switcher after I upated everything and powered up the TIU a few seconds after the egine started up. I tried to add it while it was running and it wouldn't add.
I then unplugged the AUX power and just powered it with my Z4000 and it did it again. So I shut it all down again and after restarting everything the engine acted normal. I then took the engine to my layout and it worked just fine. I have a REV L on my layout and one on my work bench. Never ran into this before.
Just thought it was ironic that after reading this post that I had it happen.
Ralph