In my case it seems that the problem is the boing updates on the 3.1 system.
Do I need them after all, if I am going for the ClassicWB install?
Ironically my 3.1 that I had on my 2.5 HDD is working flawlessly 
Also I am curious....do I really need 3.9 after all, or is enough to have just 3.1 with ClassicWB? I know that it is a matter of preferences, but I wonder if it is just a waste of time to use 3.9 (btw I have a 030/50 with 32 mb as expansion card, not even sure if that is enough to run 3.9 decently....it runs fine on my dual 8 core, but that's not fair LOL)
I have the same problem on my Amiga 1200, I got a CD-Rom on my Amiga so didn't have to install from an emulator but the BB2 rom update do not play nice so if i rename it or edit startup-sequence it boots (works in WinUAE with update).
I run ClassicWB 3.1 on my 030/42MHz 64MB ram and I have no reason to use 3.9

You can install on real amiga without a CD-rom drive using a ISO.
Just download and use this:
http://thomas-rapp.homepage.t-online.de/Start.zip (
Credit to Thomas) It also works for all CD games I have tried beside Exodus: The last war (can't even get that *?#@**?#@**?#@**?#@* to pass CD check when using a real CD and CD-rom drive)