I had a similar problem when I installed OS 3.9 on my A4000 for the first time. After the soft reset the Amiga hang with a black screen. But it continued to boot when I pressed Ctrl-A-A.
The problem disappeared after I installed Boingbag1. Now you've got a second edition CD and AFAIK the second editon already contains Boingbag1, so I don't think installing it again will cure anything.
But you can rename the AmigaOS ROM Update file in the Devs directory, then the ROM update is disabled, the soft reset will not happen and the Amiga should not hang.