I have installed OS 3.9 BB2 on my system and have not had any problems. I have a towered A4000D. My Gfx card is a PicassoIV with the newest version of Picasso96 I could find on the net.
I had installed "fresh" OS 3.5 when it can out and later OS 3.9. I had only just "discovered" BB2. It's not listed on the Amiga Inc. site and it was only after seeing it mentoned here and as a requirement for some Aminet programs that I used Google to find it at H&P.
You can give it a shot with the new update, but be prepared to boot with no startup-sequence if things go awry.
Who knows what causes things to work with one system and not others. Perhaps one of the many programs I have installed may have fixed the problem before it hit me?